scholarly journals Mercury and Other Heavy Metals Influence Bacterial Community Structure in Contaminated Tennessee Streams

2010 ◽  
Vol 77 (1) ◽  
pp. 302-311 ◽  
Author(s):  
Tatiana A. Vishnivetskaya ◽  
Jennifer J. Mosher ◽  
Anthony V. Palumbo ◽  
Zamin K. Yang ◽  
Mircea Podar ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Structure ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Inorganic Mercury ◽  
Rrna Gene ◽  
Oak Ridge

ABSTRACTHigh concentrations of uranium, inorganic mercury [Hg(II)], and methylmercury (MeHg) have been detected in streams located in the Department of Energy reservation in Oak Ridge, TN. To determine the potential effects of the surface water contamination on the microbial community composition, surface stream sediments were collected 7 times during the year, from 5 contaminated locations and 1 control stream. Fifty-nine samples were analyzed for bacterial community composition and geochemistry. Community characterization was based on GS 454 FLX pyrosequencing with 235 Mb of 16S rRNA gene sequence targeting the V4 region. Sorting and filtering of the raw reads resulted in 588,699 high-quality sequences with lengths of >200 bp. The bacterial community consisted of 23 phyla, includingProteobacteria(ranging from 22.9 to 58.5% per sample),Cyanobacteria(0.2 to 32.0%),Acidobacteria(1.6 to 30.6%),Verrucomicrobia(3.4 to 31.0%), and unclassified bacteria. Redundancy analysis indicated no significant differences in the bacterial community structure between midchannel and near-bank samples. Significant correlations were found between the bacterial community and seasonal as well as geochemical factors. Furthermore, several community members within theProteobacteriagroup that includes sulfate-reducing bacteria and within theVerrucomicrobiagroup appeared to be associated positively with Hg and MeHg. This study is the first to indicate an influence of MeHg on thein situmicrobial community and suggests possible roles of these bacteria in the Hg/MeHg cycle.

scholarly journals Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0250675
Author(s):  
Xiang Zheng ◽  
Qidi Zhu ◽  
Zhijun Zhou ◽  
Fangtong Wu ◽  
Lixuan Chen ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Structure ◽  
Feeding Habits ◽  
Bacterial Community Composition ◽  
Critical Role ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Insect Gut

Insect microbial symbioses play a critical role in insect lifecycle, and insect gut microbiome could be influenced by many factors. Studies have shown that host diet and taxonomy have a strong influence on insect gut microbial community. In this study, we performed sequencing of V3-V4 region of 16S rRNA gene to compare the composition and diversity of 12 Ensifera from 6 provinces of China. Moreover, the influences of feeding habits and taxonomic status of insects on their gut bacterial community were evaluated, which might provide reference for further application research. The results showed that Proteobacteria (45.66%), Firmicutes (34.25%) and Cyanobacteria (7.7%) were the predominant bacterial phyla in Ensifera. Moreover, the gut bacterial community composition of samples with different feeding habits was significantly different, which was irrespective of their taxa. The highest diversity of gut bacteria was found in the omnivorous Ensifera. Furthermore, common and unique bacteria with biomarkers were found based on the dietary characteristics of the samples. However, the bacterial community structure of the Ensifera samples was significantly different from that of Caelifera. Therefore, we concluded that feeding habits and taxonomic status jointly affect the gut bacterial community composition of the samples from Orthoptera. However, the influence of feeding habit dominates when taxonomy category below the suborder level. In addition, the dominant, common and unique bacterial community structure could be used to predict the contrastic feeding habits of insects belonging to Ensifera.

scholarly journals Bacterial community composition and diversity of two different forms of an organic residue of bioenergy crop

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6768
Author(s):  
Matheus A.P. Cipriano ◽  
Afnan K.A. Suleiman ◽  
Adriana P.D. da Silveira ◽  
Janaína B. do Carmo ◽  
Eiko E. Kuramae
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
16S Rrna ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Nitrous Oxide Emissions ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Microbial Composition

The use of residue of sugarcane ethanol industry named vinasse in fertirrigation is an established and widespread practice in Brazil. Both non-concentrated vinasse (NCV) and concentrated vinasse (CV) are used in fertirrigation, particularly to replace the potassium fertilizer. Although studies on the chemical and organic composition of vinasse and their impact on nitrous oxide emissions when applied in soil have been carried out, no studies have evaluated the microbial community composition and diversity in different forms of vinasse. We assessed the bacterial community composition of NCV and CV by non-culturable and culturable approaches. The non-culturable bacterial community was assessed by next generation sequencing of the 16S rRNA gene and culturable community by isolation of bacterial strains and molecular and biochemical characterization. Additionally, we assessed in the bacterial strains the presence of genes of nitrogen cycle nitrification and denitrification pathways. The microbial community based on16S rRNAsequences of NCV was overrepresented by Bacilli and Negativicutes while CV was mainly represented by Bacilli class. The isolated strains from the two types of vinasse belong to class Bacilli, similar toLysinibacillus, encode fornirKgene related to denitrification pathway. This study highlights the bacterial microbial composition particularly in CV what residue is currently recycled and recommended as a sustainable practice in sugarcane cultivation in the tropics.

scholarly journals Significant Differences in the Gut Bacterial Communities of Hooded Crane (Grus monacha) in Different Seasons at a Stopover Site on the Flyway

Animals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 701 ◽  
Author(s):  
Fengling Zhang ◽  
Xingjia Xiang ◽  
Yuanqiu Dong ◽  
Shaofei Yan ◽  
Yunwei Song ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Bacterial Community Composition ◽  
Stopover Site ◽  
Intestinal Bacterial Community ◽  
Hooded Crane ◽  
Grus Monacha

Intestinal bacterial communities form an integral component of the organism. Many factors influence gut bacterial community composition and diversity, including diet, environment and seasonality. During seasonal migration, birds use many habitats and food resources, which may influence their intestinal bacterial community structure. Hooded crane (Grus monacha) is a migrant waterbird that traverses long distances and occupies varied habitats. In this study, we investigated the diversity and differences in intestinal bacterial communities of hooded cranes over the migratory seasons. Fecal samples from hooded cranes were collected at a stopover site in two seasons (spring and fall) in Lindian, China, and at a wintering ground in Shengjin Lake, China. We analyzed bacterial communities from the fecal samples using high throughput sequencing (Illumina Mi-seq). Firmicutes, Proteobacteria, Tenericutes, Cyanobacteria, and Actinobacteria were the dominant phyla across all samples. The intestinal bacterial alpha-diversity of hooded cranes in winter was significantly higher than in fall and spring. The bacterial community composition significantly differed across the three seasons (ANOSIM, P = 0.001), suggesting that seasonal fluctuations may regulate the gut bacterial community composition of migratory birds. This study provides baseline information on the seasonal dynamics of intestinal bacterial community structure in migratory hooded cranes.

scholarly journals Ecology and Host Identity Outweigh Evolutionary History in Shaping the Bat Microbiome

mSystems ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Holly L. Lutz ◽  
Elliot W. Jackson ◽  
Paul W. Webala ◽  
Waswa S. Babyesiza ◽  
Julian C. Kerbis Peterhans ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Community Composition ◽  
Evolutionary History ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Anatomical Site ◽  
Skin Microbiota ◽  
Host Identity ◽  
Host Ecology

ABSTRACT Recent studies of mammalian microbiomes have identified strong phylogenetic effects on bacterial community composition. Bats (Mammalia: Chiroptera) are among the most speciose mammals on the planet and the only mammal capable of true flight. We examined 1,236 16S rRNA amplicon libraries of the gut, oral, and skin microbiota from 497 Afrotropical bats (representing 9 families, 20 genera, and 31 species) to assess the extent to which host ecology and phylogeny predict microbial community similarity in bats. In contrast to recent studies of host-microbe associations in other mammals, we found no correlation between chiropteran phylogeny and bacterial community dissimilarity across the three anatomical sites sampled. For all anatomical sites, we found host species identity and geographic locality to be strong predictors of microbial community composition and observed a positive correlation between elevation and bacterial richness. Last, we identified significantly different bacterial associations within the gut microbiota of insectivorous and frugivorous bats. We conclude that the gut, oral, and skin microbiota of bats are shaped predominantly by ecological factors and do not exhibit the same degree of phylosymbiosis observed in other mammals. IMPORTANCE This study is the first to provide a comprehensive survey of bacterial symbionts from multiple anatomical sites across a broad taxonomic range of Afrotropical bats, demonstrating significant associations between the bat microbiome and anatomical site, geographic locality, and host identity—but not evolutionary history. This study provides a framework for future systems biology approaches to examine host-symbiont relationships across broad taxonomic scales, emphasizing the need to elucidate the interplay between host ecology and evolutionary history in shaping the microbiome of different anatomical sites.

scholarly journals 16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248485
Author(s):  
Edith M. Muwawa ◽  
Chinedu C. Obieze ◽  
Huxley M. Makonde ◽  
Joyce M. Jefwa ◽  
James H. P. Kahindi ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Bacterial Community Composition ◽  
Geographical Location ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Chemical Parameters ◽  
Mangrove Species ◽  
Gazi Bay

Prokaryotic communities play key roles in biogeochemical transformation and cycling of nutrients in the productive mangrove ecosystem. In this study, the vertical distribution of rhizosphere bacteria was evaluated by profiling the bacterial diversity and community structure in the rhizospheres of four mangrove species (Sonneratia alba, Rhizophora mucronata, Ceriops tagal and Avicennia marina) from Mida Creek and Gazi Bay, Kenya, using DNA-metabarcoding. Alpha diversity was not significantly different between sites, but, significantly higher in the rhizospheres of S. alba and R. mucronata in Gazi Bay than in Mida Creek. Chemical parameters of the mangrove sediments significantly correlated inversely with alpha diversity metrics. The bacterial community structure was significantly differentiated by geographical location, mangrove species and sampling depth, however, differences in mangrove species and sediment chemical parameters explained more the variation in bacterial community structure. Proteobacteria (mainly Deltaproteobacteria and Gammaproteobacteria) was the dominant phylum while the families Desulfobacteraceae, Pirellulaceae and Syntrophobacteraceae were dominant in both study sites and across all mangrove species. Constrained redundancy analysis indicated that calcium, potassium, magnesium, electrical conductivity, pH, nitrogen, sodium, carbon and salinity contributed significantly to the species–environment relationship. Predicted functional profiling using PICRUSt2 revealed that pathways for sulfur and carbon metabolism were significantly enriched in Gazi Bay than Mida Creek. Overall, the results indicate that bacterial community composition and their potential function are influenced by mangrove species and a fluctuating influx of nutrients in the mangrove ecosystems of Gazi Bay and Mida Creek.

scholarly journals Colonization in the Photic Zone and Subsequent Changes during Sinking Determine Bacterial Community Composition in Marine Snow

2014 ◽  
Vol 81 (4) ◽  
pp. 1463-1471 ◽  
Author(s):  
Stefan Thiele ◽  
Bernhard M. Fuchs ◽  
Rudolf Amann ◽  
Morten H. Iversen
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Marine Snow ◽  
Free Living ◽  
Fluorescence Maximum

ABSTRACTDue to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryogel and deployed to collect intact marine snow from depths of 100 and 400 m off Cape Blanc (Mauritania). Marine snow aggregates were fixed and washedin situto prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescencein situhybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of the fluorescence maximum (20 m) but different from those at other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be “inherited” from that at the fluorescence maximum. The attached microbial community structure at 400 m differed from that of the attached community at 100 m and from that of any free-living community at the tested depths, except that collected near the sediment at 700 m. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather thande novocolonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter.

scholarly journals Bacteria associated with jellyfish during bloom and post-bloom periods

2018 ◽  
Author(s):  
Maja Kos Kramar ◽  
Tinkara Tinta ◽  
Davor Lučić ◽  
Alenka Malej ◽  
Valentina Turk
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Structure ◽  
Bacterial Community Composition ◽  
Body Part ◽  
Body Parts ◽  
Population Peak ◽  
Significant Difference ◽  
Jellyfish Population

AbstractThis study is the first to investigate bacterial community associated with live medusaAurelia sp. in the Gulf of Trieste (northern Adriatic Sea) using both culture independent and culture-based methods. We have analysed bacterial community composition of different body parts of medusa: exumbrella surface, oral arms (‘outer’ body parts) and of gastric cavity (‘inner’ body part) and investigated possible differences in medusa associated bacterial community structure at the time of jellyfish population peak and during senescent phase at the end of bloom, when jellyfish start to decay. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we demonstrated significant difference between bacterial community associated withAureliaand the ambient seawater bacterial assemblage. Comparing bacterial community composition between differentAureliamedusa body parts, communities differed significantly, especially the one within the gastral cavity. The pronounced difference is dominance ofBetaproteobacteria(Burkholderia, CupriavidusandAchromobacter) in gastral cavity of medusa andAlpha- (Phaeobacter, Ruegeria) andGamma-proteobacteria(Stenotrophomonas, Alteromonas, PseudoalteromonasandVibrio) on ‘outer’ body parts. This suggests that body-part specific bacterial association might have an important functional roles for the host. The results of bacterial isolates showed the dominance ofGammaproeteobacteria, especiallyVibrioandPseudoalteromonasin all body parts. Finally, comparison of medusa associated bacterial community structure, at the time of jellyfish population peak and during senescent phase at the end of bloom showed increased abundance ofGammaproteobacteria, especiallyVibrio. Our results suggest members ofVibriogroup are possible commensal opportunistic visitors, later becoming consumer of moribund jellyfish biomass and that the structure of jellyfish bacterial community might be affected by anthropogenic pollution in the marine environment.

scholarly journals Effect of Methane Inhibitors on Ruminal Microbiota During Early Life and Its Relationship With Ruminal Metabolism and Growth in Calves

2021 ◽  
Vol 12 ◽  
Author(s):  
Omar Cristobal-Carballo ◽  
Susan A. McCoard ◽  
Adrian L. Cookson ◽  
Siva Ganesh ◽  
Katherine Lowe ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Community Composition ◽  
Early Life ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Metabolite Profile ◽  
Treatment Groups ◽  
Methanogen Community ◽  
And Performance

The present study aimed to determine whether dietary supplementation with methanogen inhibitors during early life may lead to an imprint on the rumen microbial community and change the rumen function and performance of calves to 49-weeks of rearing. Twenty-four 4-day-old Friesian x Jersey cross calves were randomly assigned into a control and a treatment group. Treated calves were fed a combination of chloroform (CF) and 9,10-anthraquinone (AQ) in the solid diets during the first 12 weeks of rearing. Afterward, calves were grouped by treatments until week 14, and then managed as a single group on pasture. Solid diets and water were offered ad libitum. Methane measurements, and sample collections for rumen metabolite and microbial community composition were carried out at the end of weeks 2, 4, 6, 8, 10, 14, 24 and 49. Animal growth and dry matter intake (DMI) were regularly monitored over the duration of the experiment. Methane emissions decreased up to 90% whilst hydrogen emissions increased in treated compared to control calves, but only for up to 2 weeks after treatment cessation. The near complete methane inhibition did not affect calves’ DMI and growth. The acetate:propionate ratio decreased in treated compared to control calves during the first 14 weeks but was similar at weeks 24 and 49. The proportions of Methanobrevibacter and Methanosphaera decreased in treated compared to control calves during the first 14 weeks; however, at week 24 and 49 the archaea community was similar between groups. Bacterial proportions at the phylum level and the abundant bacterial genera were similar between treatment groups. In summary, methane inhibition increased hydrogen emissions, altered the methanogen community and changed the rumen metabolite profile without major effects on the bacterial community composition. This indicated that the main response of the bacterial community was not a change in composition but rather a change in metabolic pathways. Furthermore, once methane inhibition ceased the methanogen community, rumen metabolites and hydrogen emissions became similar between treatment groups, indicating that perhaps using the treatments tested in this study, it is not possible to imprint a low methane microbiota into the rumen in the solid feed of pre-weaned calves.

scholarly journals Impact of enzymatic digestion on bacterial community composition in CF airway samples

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3362 ◽  
Author(s):  
Kayla M. Williamson ◽  
Brandie D. Wagner ◽  
Charles E. Robertson ◽  
Emily J. Johnson ◽  
Edith T. Zemanick ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Dna Extraction ◽  
Community Composition ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Diversity Index ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Enzymatic Digestion ◽  
Rrna Gene

BackgroundPrevious studies have demonstrated the importance of DNA extraction methods for molecular detection ofStaphylococcus,an important bacterial group in cystic fibrosis (CF). We sought to evaluate the effect of enzymatic digestion (EnzD) prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP) samples from patients with CF.MethodsDNA from 81 samples (39 sputum and 42 OP) collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA) was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA) of individual genera for paired samples with and without EnzD.ResultsShannon Diversity Index (alpha-diversity) decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn), whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the generaGemella(p < 0.01),Streptococcus(p < 0.01), andRothia(p < 0.01).Staphylococcus(p < 0.01) was the only genus with a significant increase in RA from sputum, whereas the following genera decreased in RA with EnzD:Veillonella(p < 0.01),Granulicatella(p < 0.01),Prevotella(p < 0.01), andGemella(p = 0.02). In OP samples, higher RA of Gram-positive taxa was associated with larger changes in microbial community composition.DiscussionWe show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection ofStaphylococcusin CF OP samples. The enhanced identification ofStaphylococcus aureusis a strong indication to utilize EnzD in studies that use OP swabs to monitor CF airway communities.

scholarly journals Effect of Sheep Urine Deposition on the Bacterial Community Structure in an Acidic Upland Grassland Soil

2006 ◽  
Vol 72 (11) ◽  
pp. 7231-7237 ◽  
Author(s):  
Deirdre Rooney ◽  
Nabla Kennedy ◽  
Louise Deering ◽  
Deirdre Gleeson ◽  
Nicholas Clipson
Keyword(s):  
Community Structure ◽  
Microbial Biomass ◽  
Bacterial Community ◽  
Microbial Activity ◽  
Community Composition ◽  
Plant Species ◽  
Bacterial Community Structure ◽  
Bacterial Community Composition ◽  
High Concentrations ◽  
Sheep Urine

ABSTRACT The effect of the addition of synthetic sheep urine (SSU) and plant species on the bacterial community composition of upland acidic grasslands was studied using a microcosm approach. Low, medium, and high concentrations of SSU were applied to pots containing plant species typical of both unimproved (Agrostis capillaris) and agriculturally improved (Lolium perenne) grasslands, and harvests were carried out 10 days and 50 days after the addition of SSU. SSU application significantly increased both soil pH (P < 0.005), with pH values ranging from pH 5.4 (zero SSU) to pH 6.4 (high SSU), and microbial activity (P < 0.005), with treatment with medium and high levels of SSU displaying significantly higher microbial activity (triphenylformazan dehydrogenase activity) than treatment of soil with zero or low concentrations of SSU. Microbial biomass, however, was not significantly altered by any of the SSU applications. Plant species alone had no effect on microbial biomass or activity. Bacterial community structure was profiled using bacterial automated ribosomal intergenic spacer analysis. Multidimensional scaling plots indicated that applications of high concentrations of SSU significantly altered the bacterial community composition in the presence of plant species but at different times: 10 days after application of high concentrations of SSU, the bacterial community composition of L. perenne-planted soils differed significantly from those of any other soils, whereas in the case of A. capillaris-planted soils, the bacterial community composition was different 50 days after treatment with high concentrations of SSU. Canonical correspondence analysis also highlighted the importance of interactions between SSU addition, plant species, and time in the bacterial community structure. This study has shown that the response of plants and bacterial communities to sheep urine deposition in grasslands is dependent on both the grass species present and the concentration of SSU applied, which may have important ecological consequences for agricultural grasslands.

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