scholarly journals The role of macrobiota in structuring microbial communities along rocky shores

2014 ◽  
Author(s):  
Catherine A Pfister ◽  
Jack A Gilbert ◽  
Sean M Gibbons
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Rocky Shore ◽  
Alpha Diversity ◽  
Rocky Shores ◽  
Microbial Composition ◽  
Habitat Specificity ◽  
Microbial Habitat ◽  
Inert Surfaces

Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.

scholarly journals The role of macrobiota in structuring microbial communities along rocky shores

2014 ◽  
Author(s):  
Catherine A Pfister ◽  
Jack A Gilbert ◽  
Sean M Gibbons
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Rocky Shore ◽  
Alpha Diversity ◽  
Rocky Shores ◽  
Microbial Composition ◽  
Habitat Specificity ◽  
Microbial Habitat ◽  
Inert Surfaces

Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.

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 Fecal Microbial Diversity and Structure Are Associated with Diet Quality in the Multiethnic Cohort Adiposity Phenotype Study

2019 ◽  
Vol 149 (9) ◽  
pp. 1575-1584 ◽  
Author(s):  
Gertraud Maskarinec ◽  
Meredith A J Hullar ◽  
Kristine R Monroe ◽  
John A Shepherd ◽  
Jeani Hunt ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Healthy Eating ◽  
Diet Quality ◽  
Microbial Community Structure ◽  
Alpha Diversity ◽  
Clinic Visit ◽  
Healthy Eating Index ◽  
Dietary Index ◽  
Multiethnic Cohort

ABSTRACT Background Variation in gut microbial community structure is partly attributed to variations in diet. A priori dietary indexes capture diet quality and have been associated with chronic disease risk. Objectives The aim of this study was to examine the association of diet quality, as assessed by the Healthy Eating Index, Alternative Healthy Eating Index-2010, alternate Mediterranean Diet, and the Dietary Approaches to Stop Hypertension Trial, with measures of fecal microbial community structure assessed in the Adiposity Phenotype Study (APS), an ethnically diverse study population with varied food intakes. Methods Multiethnic Cohort Study members completed a validated quantitative food frequency questionnaire (QFFQ) at cohort entry (1993–1996) and, for the APS subset, at clinic visit (2013–2015), when they also provided a stool sample. DNA was extracted from stool, and the V1-V3 region of the 16S rRNA gene was amplified and sequenced. Dietary index scores were computed based on the QFFQ and an extensive nutritional database. Using linear regression adjusted for relevant covariates, we estimated associations of dietary quality with microbiome measures and computed adjusted mean values of microbial measures by tertiles of dietary index scores. Results The 858 men and 877 women of white, Japanese American, Latino, Native Hawaiian, and African American ancestry had a mean age of 69.2 years at stool collection. Alpha diversity according to the Shannon index increased by 1–2% across tertiles of all 4 diet indexes measured at clinic visit. The mean relative abundance of the phylum Actinobacteria was 13–19% lower with higher diet quality across all 4 indexes (difference between tertile 3 and tertile 1 divided by tertile 1). Of the 104 bacterial genera tested, 21 (primarily from the phylum Firmicutes) were positively associated with at least 1 index after Bonferroni adjustment. Conclusion Diet quality was strongly associated with fecal microbial alpha diversity and beta diversity and several genera previously associated with human health.

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 Disentangling race, environment and the microbiome in a study of preterm birth risk

2021 ◽  
Author(s):  
Shan Sun ◽  
Myrna Serrano ◽  
Jennifer Fettweis ◽  
Patricia Basta ◽  
Emma Rosen ◽  
...  
Keyword(s):  
Community Structure ◽  
Preterm Birth ◽  
Microbial Community ◽  
Black Women ◽  
Microbial Community Structure ◽  
White Women ◽  
Alpha Diversity ◽  
Term Birth ◽  
Lower Abundance ◽  
Microbial Biomarkers

Abstract Previous studies have investigated the associations between the vaginal microbiome and preterm birth (PTB), with the aim of determining whether differences in community patterns meaningfully alter risk, and could therefore be the target of intervention. We report on vaginal microbial analysis on a subset of the Pregnancy, Infection, and Nutrition (PIN) Study, a prospectively enrolled cohort of women in central North Carolina between 1995-2001. We selected a nested case-control subset of this cohort, including 464 White women (375 term birth and 89 spontaneous PTB, sPTB) and 360 Black women (276 term birth and 84 sPTB). Microbial DNA was extracted from genital track swabs collected mid-pregnancy, and subjected to 16S rRNA taxonomic profiling. We found that microbial community structure is associated with race and sPTB, although the influence of race is stronger than the influence of sPTB. The microbiome of Black women has higher alpha-diversity, higher abundance of Lactobacillus iners and lower abundance of Lactobacillus crispatus. These differences were obscured once maternal douching behavior was considered—specifically, among women who douche, there were no significant differences in microbiome by race. The sPTB associated microbiome exhibited a lower abundance of L. crispatus, while alpha diversity and L. iners were not significantly different. Associations between the microbiome and sPTB were only significant in women who do not douche. While race was a strong predictor of microbial community structure, we also observed strong intercorrelations between a range of maternal factors, including poverty, education, marital status, age, douching and race, with microbiome effect sizes in the range of 1.8-5.2% in univariate models. Therefore, race may simply be a proxy for other socially driven factors that differentiate microbiome community structures. Future work will continue to refine reliable microbial biomarkers for preterm birth across diverse cohorts.

scholarly journals The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260121
Author(s):  
Hiroki Morita ◽  
Satoshi Akao
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Sample Size ◽  
Soil Sample ◽  
Dna Extraction ◽  
Microbial Community Structure ◽  
Diversity Index ◽  
Sample Sizes ◽  
Microbial Composition ◽  
Taxonomic Rank

To determine the optimal soil sample size for microbial community structure analysis, DNA extraction, microbial composition analysis, and diversity assessments were performed using soil sample sizes of 0.2, 1, and 5 g. This study focused on the relationship between soil amount and DNA extraction container volume and the alteration in microbial composition at different taxonomic ranks (order, class, and phylum). Horizontal (0.2 and 1 g) and vertical (5 g) shaking were applied during DNA extraction for practical use in a small laboratory. In the case of the 5 g soil sample, DNA extraction efficiency and the value of α-diversity index fluctuated severely, possibly because of vertical shaking. Regarding the 0.2 and 1 g soil samples, the number of taxa, Shannon–Wiener index, and Bray–Curtis dissimilarity were stable and had approximately the same values at each taxonomic rank. However, non-metric multidimensional scaling showed that the microbial compositions of these two sample sizes were different. The higher relative abundance of taxa in the case of the 0.2 g soil sample might indicate that cell wall compositions differentiated the microbial community structures in these two sample sizes due to high shear stress tolerance. The soil sample size and tube volume affected the estimated microbial community structure. A soil sample size of 0.2 g would be preferable to the other sample sizes because of the possible higher shearing force for DNA extraction and lower experimental costs due to smaller amounts of consumables. When the taxonomic rank was changed from order to phylum, some minor taxa identified at the order rank were integrated into major taxa at the phylum rank. The integration affected the value of the β-diversity index; therefore, the microbial community structure analysis, reproducibility of structures, diversity assessment, and detection of minor taxa would be influenced by the taxonomic rank applied.

scholarly journals Preliminary Assessment of Microbial Community Structure of Wind-Tidal Flats in the Laguna Madre, Texas, USA

Biology ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 183 ◽  
Author(s):  
I.-Shuo Huang ◽  
Lee J. Pinnell ◽  
Jeffrey W. Turner ◽  
Hussain Abdulla ◽  
Lauren Boyd ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Genomic Analysis ◽  
Tidal Flats ◽  
Bioactive Metabolites ◽  
Laguna Madre ◽  
Microbial Composition ◽  
Field Station ◽  
Two Samples

Aside from two samples collected nearly 50 years ago, little is known about the microbial composition of wind tidal flats in the hypersaline Laguna Madre, Texas. These mats account for ~42% of the lagoon’s area. These microbial communities were sampled at four locations that historically had mats in the Laguna Madre, including Laguna Madre Field Station (LMFS), Nighthawk Bay (NH), and two locations in Kenedy Ranch (KRN and KRS). Amplicon sequencing of 16S genes determined the presence of 51 prokaryotic phyla dominated by Bacteroidota, Chloroflexi, Cyanobacteria, Desulfobacteria, Firmicutes, Halobacteria, and Proteobacteria. The microbial community structure of NH and KR is significantly different to LMFS, in which Bacteroidota and Proteobacteria were most abundant. Twenty-three cyanobacterial taxa were identified via genomic analysis, whereas 45 cyanobacterial taxa were identified using morphological analysis, containing large filamentous forms on the surface, and smaller, motile filamentous and coccoid forms in subsurface mat layers. Sample sites were dominated by species in Oscillatoriaceae (i.e., Lyngbya) and Coleofasciculaceae (i.e., Coleofasciculus). Most cyanobacterial sequences (~35%) could not be assigned to any established taxa at the family/genus level, given the limited knowledge of hypersaline cyanobacteria. A total of 73 cyanobacterial bioactive metabolites were identified using ultra performance liquid chromatography-Orbitrap MS analysis from these commu nities. Laguna Madre seems unique compared to other sabkhas in terms of its microbiology.

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 Relationships Between the Microbial Composition and the Geochemistry and Mineralogy of the Cobalt-Bearing Legacy Mine Tailings in Northeastern Ontario

2021 ◽  
Vol 12 ◽  
Author(s):  
Brittaney Courchesne ◽  
Michael Schindler ◽  
Nadia C. S. Mykytczuk
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Mine Tailings ◽  
Mine Drainage ◽  
Lower Amount ◽  
Critical Element ◽  
Biogeochemical Processes ◽  
Microbial Composition ◽  
Average Valence

Mine tailings host dynamic biogeochemical processes that can mobilize a range of elements from the host material and release them into the environment through acidic, neutral, or alkaline mine drainage. Here we use a combination of mineralogical, geochemical, and microbiological techniques that provide a better understanding of biogeochemical processes within the surficial layers of neutral cobalt and arsenic-rich tailings material at Cobalt, ON, Canada. Tailings material within 30-cm depth profiles from three tailings sites (sites A, B, and C) were characterized for their mineralogical, chemical and microbial community compositions. The tailings material at all sites contains (sulf)arsenides (safflorite, arsenopyrite), and arsenates (erythrite and annabergite). Site A contained a higher and lower amount of (sulf)arsenides and arsenates than site B, respectively. Contrary to site A and B, site C depicted a distinct zoning with (sulf)arsenides found in the deeper reduced zone, and arsenates occurring in the shallow oxidized zone. Variations in the abundance of Co+As+Sb+Zn (Co#), Fe (Fe#), total S (S#), and average valence of As indicated differences in the mineralogical composition of the tailings material. For example, material with a high Co#, lo Fe# and high average valence of As commonly have a higher proportion of secondary arsenate to primary (sulf)arsenide minerals. Microbial community profiling indicated that the Cobalt tailings are primarily composed of Actinobacteria and Proteobacteria, and known N, S, Fe, methane, and possible As-cycling bacteria. The tailings from sites B and C had a larger abundance of Fe and S-cycling bacteria (e.g., Sulfurifustis and Thiobacillus), which are more abundant at greater depths, whereas the tailings of site A had a higher proportion of potential As-cycling and -resistant genera (e.g., Methylocystis and Sphingomonas). A multi-variate statistical analysis showed that (1) distinct site-specific groupings occur for the Co # vs. Fe #, Co# vs. S#’s and for the microbial community structure and (2) microbial communities are statistically highly correlated to depth, S#, Fe#, pH and the average valence of As. The variation in As valence correlated well with the abundance of N, S, Fe, and methane-cycling bacteria. The results of this study provide insights into the complex interplay between minerals containing the critical element cobalt, arsenic, and microbial community structure in the Cobalt Mining Camp tailings.

scholarly journals Effects of Freezing-Thawing on Microbial Community Structure in the Soil of Old Apple Orchards

HortScience ◽  
2021 ◽  
pp. 1-7
Author(s):  
Haiyan Wang ◽  
Rong Zhang ◽  
Weitao Jiang ◽  
Yunfei Mao ◽  
Xuesen Chen ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Alpha Diversity ◽  
Apple Orchards ◽  
Soil Layers ◽  
Soil Microbial ◽  
Average Temperature ◽  
Abundance And Diversity ◽  
The Relationship

The study here aimed to investigate the effects of pre-winter ditching and freezing-thawing on soil microbial structure in different soil layers of old apple orchards. A total of 30 samples were obtained from 3 Nov. 2016 to 9 Mar. 2017. The relative abundance, alpha diversity, community structure of fungi, and the relationship between environmental factors and microbial community structure were analyzed, and the greenhouse experiments were used for further verification. Results showed that the number of actinomycete and total bacterial colonies decreased, whereas the number of fungi sustained decreased, resulting in a higher bacteria/fungi ratio. The percentage of Fusarium initially decreased, then later increased by 11.38%, 3.469%, 2.35%, 2.29%, and 3.09%. However, Fusarium levels were still 9% lower on 9 Mar. 2017 that on 3 Nov. 2016. Both the abundance and diversity of the community were higher in the upper soil than in the lower. The main environmental factor contributing to the percentage of Fusarium change was average temperature (AT), although highest temperature (HT) and water content (WC) also had an impact. The Malus hupehensis Rehd. seedlings growing in lower soil were more vigorous than that in upper soil. In sum, pre-winter ditching and freezing-thawing in old apple orchards can reduce the abundance percentage of harmful Fusarium and promote the growth of M. hupehensis Rehd. seedlings.

Sign in / Sign up

Export Citation Format

Share Document