scholarly journals Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3075 ◽  
Author(s):  
Sheila Torres ◽  
Jonathan B. Clayton ◽  
Jessica L. Danzeisen ◽  
Tonya Ward ◽  
Hu Huang ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Skin Microbiome ◽  
Bacterial Populations ◽  
Operational Taxonomic Units ◽  
Hair Type ◽  
Different Seasons ◽  
Over Time

It has previously been shown that domestic dogs and their household owners share bacterial populations, and that sharing of bacteria between humans is facilitated through the presence of dogs in the household. However, less is known regarding the bacterial communities of dogs, how these communities vary by location and over time, and how cohabitation of dogs themselves influences their bacterial community. Furthermore, the effects of factors such as breed, hair coat length, sex, shedding, and age on the canine skin microbiome is unknown. This study sampled the skin bacterial communities of 40 dogs belonging to 20 households longitudinally across three seasons (spring, summer, and winter). Significant differences in bacterial community structure between samples were identified when stratified by season, but not by dog sex, age, breed, hair type, or skin site. Cohabitating dogs were more likely to share bacteria of the skin than non-cohabitating dogs. Similar to human bacterial microbiomes, dogs’ microbiomes were more similar to their own microbiomes over time than to microbiomes of other individuals. Dogs sampled during the same season were also more similar to each other than to dogs from different seasons, irrespective of household. However, there were very few core operational taxonomic units (OTUs) identified across all dogs sampled. Taxonomic classification revealedPropionibacterium acnesandHaemophilussp. as key members of the dog skin bacterial community, along withCorynebacteriumsp. andStaphylococcus epidermidis. This study shows that the skin bacterial community structure of dogs is highly individualized, but can be shared among dogs through cohabitation.

scholarly journals Effects of Plastic Debris on the Biofilm Bacterial Communities in Lake Water

Water ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1465
Author(s):  
Chao Shen ◽  
Liuyan Huang ◽  
Guangwu Xie ◽  
Yulai Wang ◽  
Zongkai Ma ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Diversity Index ◽  
Plastic Substrate ◽  
Simpson Index ◽  
Plastic Debris ◽  
Plastic Substrates ◽  
Wiener Diversity Index

Increasing discharge of plastic debris into aquatic ecosystems and the worsening ecological risks have received growing attention. Once released, plastic debris could serve as a new substrate for microbes in waters. The complex relationship between plastics and biofilms has aroused great interest. To confirm the hypothesis that the presence of plastic in water affects the composition of biofilm in natural state, in situ biofilm culture experiments were conducted in a lake for 40 days. The diversity of biofilm attached on natural (cobble stones (CS) and wood) and plastic substrates (Polyethylene terephthalate (PET) and Polymethyl methacrylate (PMMA)) were compared, and the community structure and composition were also analyzed. Results from high-throughput sequencing of 16S rRNA showed that the diversity and species richness of biofilm bacterial communities on natural substrate (observed species of 1353~1945, Simpson index of 0.977~0.989 and Shannon–Wiener diversity index of 7.42~8.60) were much higher than those on plastic substrates (observed species of 900~1146, Simpson index of 0.914~0.975 and Shannon–Wiener diversity index of 5.47~6.99). The NMDS analyses were used to confirm the taxonomic significance between different samples, and Anosim (p = 0.001, R = 0.892) and Adonis (p = 0.001, R = 808, F = 11.19) demonstrated that this classification was statistically rigorous. Different dominant bacterial communities were found on plastic and natural substrates. Alphaproteobacterial, Betaproteobacteria and Synechococcophycideae dominated on the plastic substrate, while Gammaproteobacteria, Phycisphaerae and Planctomycetia played the main role on the natural substrates. The bacterial community structure of the two substrates also showed significant difference which is consistent with previous studies using other polymer types. Our results shed light on the fact that plastic debris can serve as a new habitat for biofilm colonization, unlike natural substrates, pathogens and plastic-degrading microorganisms selectively attached to plastic substrates, which affected the bacterial community structure and composition in aquatic environment. This study provided a new insight into understanding the potential impacts of plastics serving as a new habitat for microbial communities in freshwater environments. Future research should focus on the potential impacts of plastic-attached biofilms in various aquatic environments and the whole life cycle of plastics (i.e., from plastic fragments to microplastics) and also microbial flock characteristics using microbial plastics in the natural environment should also be addressed.

Molecular Analysis of Bacterial Community Structure and Diversity in Unimproved and Improved Upland Grass Pastures

1999 ◽  
Vol 65 (4) ◽  
pp. 1721-1730 ◽  
Author(s):  
Allison E. McCaig ◽  
L. Anne Glover ◽  
James I. Prosser
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Sequence Similarity ◽  
Soil Samples ◽  
Operational Taxonomic Units ◽  
16S Ribosomal Dna ◽  
Pcr Products ◽  
Evenness Indices ◽  
Low Coverage

ABSTRACT Bacterial community structure and diversity in rhizospheres in two types of grassland, distinguished by both plant species and fertilization regimen, were assessed by performing a 16S ribosomal DNA (rDNA) sequence analysis of DNAs extracted from triplicate soil plots. PCR products were cloned, and 45 to 48 clones from each of the six libraries were partially sequenced. Phylogenetic analysis of the resultant 275 clone sequences indicated that there was considerable variation in abundance in replicate unfertilized, unimproved soil samples and fertilized, improved soil samples but that there were no significant differences in the abundance of any phylogenetic group. Several clone sequences were identical in the 16S rDNA region analyzed, and the clones comprised eight pairs of duplicate clones and two sets of triplicate clones. Many clones were found to be most closely related to environmental clones obtained in other studies, although three clones were found to be identical to culturable species in databases. The clones were clustered into operational taxonomic units at a level of sequence similarity of >97% in order to quantify diversity. In all, 34 clusters containing two or more sequences were identified, and the largest group contained nine clones. A number of diversity, dominance, and evenness indices were calculated, and they all indicated that diversity was high, reflecting the low coverage of rDNA libraries achieved. Differences in diversity between sample types were not observed. Collector’s curves, however, indicated that there were differences in the underlying community structures; in particular, there was reduced diversity of organisms of the α subdivision of the class Proteobacteria (α-proteobacteria) in improved soils.

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 Comparative analysis of the composition of bacterial communities from two constructed wetlands for municipal and swine wastewater treatment

2009 ◽  
Vol 8 (1) ◽  
pp. 147-157 ◽  
Author(s):  
Paula Arroyo ◽  
Gemma Ansola ◽  
Ivan Blanco ◽  
Patricia Molleda ◽  
Estanislao de Luis Calabuig ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Typha Latifolia ◽  
Treatment System ◽  
Swine Wastewater ◽  
Wastewater Treatment System ◽  
Wastewater Treatment Systems

This work provides information about bacterial community structure in natural wastewater treatment systems treating different types of wastewater. The diversity and composition of bacterial communities associated with the rhizosphere of Typha latifolia and Salix atrocinerea were studied and compared among two different natural wastewater treatment systems, using the direct sequencing of the 16S ribosomal RNA codifying genes. Phylogenetic affiliations of the bacteria detected allowed us to define the main groups present in these particular ecosystems. Moreover, bacterial community structure was studied through two diversity indices. Ten identified and five non-identified phyla were found in the samples; the phylum Proteobacteria was the predominant group in the four ecosystems. The results showed a bacterial community dominated by beta-proteobacteria and a lower diversity value in the swine wastewater treatment system. The municipal wastewater treatment system presented a high diverse community in both macrophytes (Typha latifolia and Salix atrocinerea), with gamma-proteobacteria and alpha-proteobacteria, respectively, as the most abundant groups.

Effects of Long-Term Elevated CO2 on Rhizosphere and Bulk Soil Bacterial Community Structure in Pinus sylvestriformis Seedlings Fields

2011 ◽  
Vol 343-344 ◽  
pp. 351-356
Author(s):  
Xia Jia ◽  
Chun Juan Zhou
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pinus Sylvestriformis ◽  
Soil Bacterial Community Structure ◽  
Gradient Gel Electrophoresis ◽  
Polymerase Chain

The effect of long-term elevated CO2(as open top chambers) on rhizosphere and bulk bacterial community structure in Pinus sylvestriformis seedlings field was investigated in July, August, and September. The bacterial communities were processed by Denaturing Gradient Gel Electrophoresis (DGGE) analysis of bacterial 16S rDNA fragments amplified by PCR (Polymerase Chain Reaction) from DNA extracted directly from soil. DGGE profiles from rhizosphere samples showed large changes in rhizosphere bacterial community under elevated CO2compared to ambient except for that in September. For bulk samples, bacterial community structure changed when exposed to elevated CO2in three months. With the exception of bulk samples in August, a similitude of bacterial communities structures existed between different elevated CO2concentrations by analyzing UPGMA dendrogram based on Jaccard’s coefficient.

scholarly journals TiO2 nanoparticles affect the bacterial community structure and Eisenia fetida (Savigny, 1826) in an arable soil

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6939 ◽  
Author(s):  
Katia Berenice Sánchez-López ◽  
Francisco J. De los Santos-Ramos ◽  
Elizabeth Selene Gómez-Acata ◽  
Marco Luna-Guido ◽  
Yendi E. Navarro-Noya ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Organic Material ◽  
Eisenia Fetida ◽  
Bacterial Community Structure ◽  
Arable Soil ◽  
Unamended Soil ◽  
Oat Seeds ◽  
Dry Soil ◽  
Over Time

The amount of nanoparticles (NP), such as TiO2, has increased substantially in the environment. It is still largely unknown, however, how NP might interact with earthworms and organic material and how this might affect the bacterial community structure and their functionality. Therefore, an arable soil was amended with TiO2 NP at 0, 150 or 300 mg kg−1 and subjected to different treatments. Treatments were soil amended with ten earthworms (Eisenia fetida (Savigny, 1826)) with fully developed clitellum and an average fresh mass of 0.5 to 500 g dry soil, 1.75 g tyndallized Quaker® oat seeds Avena sativa (L.) kg−1, or earthworms plus oat seeds, or left unamended. The bacterial community structure was monitored throughout the incubation period. The bacterial community in the unamended soil changed over time and application of oats, earthworm and a combination of both even further, with the largest change found in the latter. Application of NP to the unamended soil and the earthworm-amended soil altered the bacterial community, but combining it by adding oats negated that effect. It was found that the application of organic material, that is, oats, reduced the effect of the NP applied to soil. However, as the organic material applied was mineralized by the soil microorganisms, the effect of NP increased again over time.

scholarly journals Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2367 ◽  
Author(s):  
Isabelle Laforest-Lapointe ◽  
Christian Messier ◽  
Steven W. Kembel
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Individual Variation ◽  
Host Species ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Temperate Forest ◽  
Abies Balsamea ◽  
Tree Canopy ◽  
Individual Tree

BackgroundThe diversity and composition of the microbial community of tree leaves (the phyllosphere) varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada.MethodsWe targeted five dominant temperate forest tree species including angiosperms and gymnosperms:Acer saccharum,Acer rubrum,Betula papyrifera,Abies balsameaandPicea glauca. For one randomly selected tree of each species, we sampled microbial communities at six distinct canopy locations: bottom-canopy (1–2 m height), the four cardinal points of mid-canopy (2–4 m height), and the top-canopy (4–6 m height). We also collected bottom-canopy leaves from five additional trees from each species.ResultsBased on an analysis of bacterial community structure measured via Illumina sequencing of the bacterial 16S gene, we demonstrate that 65% of the intra-individual variation in leaf bacterial community structure could be attributed to the effect of inter-individual and inter-specific differences while the effect of canopy location was not significant. In comparison, host species identity explains 47% of inter-individual and inter-specific variation in leaf bacterial community structure followed by individual identity (32%) and canopy location (6%).DiscussionOur results suggest that individual samples from consistent positions within the tree canopy from multiple individuals per species can be used to accurately quantify variation in phyllosphere bacterial community structure. However, the considerable amount of intra-individual variation within a tree canopy ask for a better understanding of how changes in leaf characteristics and local abiotic conditions drive spatial variation in the phyllosphere microbiome.

scholarly journals Difference in Rhizosphere Soil Bacterial Community was among Six Cinnamomum camphora Chemotypes

2021 ◽  
Author(s):  
Zufei Xiao ◽  
Beihong Zhang ◽  
Yangbao Wang ◽  
Zhinong Jin ◽  
Feng Li ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Rhizosphere Soil ◽  
Soil Nutrient ◽  
Soil Bacterial Community ◽  
Cinnamomum Camphora ◽  
Close Relationship ◽  
Soil Bacterial

Abstract: Plant types and soil bacterial communities had a close relationship, understanding the profound association between them contributes to better learn bacterial ecological function for plant growth. In this study, rhizosphere soil of six different chemotype Cinnamomum camphora trees were collected, including C. bodinieri var. citralifera, [C. camphora (Linn.) Presl], camphora-type, cineole-type, linalool-type and isoborneol-type. Soil properties content and bacterial communities were analyzed. Two chemotype C. camphora, including [C. camphora (Linn.) Presl] and linalool-type, shaped similar bacterial community structure, decreased Firmcutes relative abundance. richness estimators (Chao1 index and Ace index) of [C. camphora (Linn.) Presl] were decreased compared with the others. Furthermore, soil bacterial community structure was also similar among bodinieri var. citralifera, camphora-type, cineole-type and isoborneol-type. Hence, different chemotype C. camphora altered soil nutrient and shaped rhizosphere bacterial communities.

scholarly journals Variation of rhizosphere bacterial community diversity in the desert ephemeral plant Ferula sinkiangensis across environmental gradients

2020 ◽  
Author(s):  
Zhang tao ◽  
Wang Zhongke ◽  
Lv Xinhua ◽  
Dang Hanli ◽  
Zhuang Li
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Community Diversity ◽  
Bacterial Community Diversity ◽  
Physicochemical Factors ◽  
Rhizosphere Bacterial Community ◽  
Ferula Sinkiangensis ◽  
Rhizosphere Bacterial Communities

Ferula sinkiangensis is a desert short-lived medicinal plant, and its number is rapidly decreasing. Rhizosphere microbial community plays an important role in plant growth and adaptability. However, Ferula sinkiangensis rhizosphere bacterial communities and the soil physicochemical factors that drive the bacterial community distribution are currently unclear. On this study, based on high-throughput sequencing, we explored the diversity, structure and composition of Ferula sinkiangensis rhizosphere bacterial communities at different slope positions and soil depths and their correlation with soil physicochemical properties. Our results revealed the heterogeneity and variation trends of Ferula sinkiangensis rhizosphere bacterial community diversity and abundance on a fine spatial scale (Slope position and soil depth) and Found Actinobacteria (25.5%), Acidobacteria (16.9%), Proteobacteria (16.6%), Gemmatimonadetes (11.5%) and Bacteroidetes (5.8%) were the dominant bacterial phyla in Ferula sinkiangensi s rhizosphere soil. Among all soil physicochemical variables shown in this study, there was a strong positive correlation between phosphorus (AP) and the diversity of rhizosphere bacterial community in Ferula sinkiangensis . In addition, Soil physicochemical factors jointly explained 24.28% of variation in Ferula sinkiangensis rhizosphere bacterial community structure. Among them, pH largely explained the variation of Ferula sinkiangensis rhizosphere bacterial community structure (5.58%), followed by total salt (TS, 5.21%) and phosphorus (TP, 4.90%).

scholarly journals Effects of ultraviolet radiation on the community structure and metabolic pathways of A2O process at Plateau environment

2021 ◽  
Author(s):  
Zong Yongchen ◽  
He Qiang ◽  
Guo Mingzhe ◽  
You Junhao ◽  
Zhang Dongyan
Keyword(s):  
Community Structure ◽  
Water Treatment ◽  
Bacterial Community ◽  
Ultraviolet Radiation ◽  
Relative Abundance ◽  
Ultraviolet Irradiation ◽  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Bacterial Community Structure ◽  
Key Species

Abstract Water treatment ecosystem provides important habitats for various bacterial communities. However, the response mechanism of this ecosystem under ultraviolet rays is not yet clear. In the study, 16S rRNA gene sequencing is used to study the bacterial community structure and metabolic pathways under 5 samples of ultraviolet irradiation times. In general, the bacterial communities of the five samples are different, which indicates that the ultraviolet radiation time has an impact on the bacterial community structure. Analysis of driving factors shows that UV, COD, pH, TN and NH3-N have an impact on the relative abundance of key species. Key species under ultraviolet irradiation are Bacteroidetes, Proteobacteria, Actinobacteria, Firmicutes, Chloroflexi, and Chlamydiae, accounting for 96.69%ཞ98.30%, and ultraviolet irradiation has a significant inhibitory effect on the relative abundance. As the dominant bacterial phyla in Plateau environment, Chlamydiae is discovered for the first time. The network co-occurrence diagrams constructed under different ultraviolet radiation show that each sample is composed of three independent network diagrams. There are 6 common dominant phyla and 33 common dominant bacterial genera in each sample, which reveals that the structure of the ecosystem is composed of more similar microorganisms, rather than random phenomena. It also reflects the competitive relationship between species and the adaptability of bacteria to the environment. Through the analysis of metabolic pathways, it is found that the dominant metabolic pathways in high altitude habitats have certain changes under ultraviolet radiation. Further analysis of carbon, nitrogen and phosphorus metabolic pathways shows that the relative abundance of related metabolic pathways has a certain change, but the difference in metabolic maps is small, that is, the effect of ultraviolet radiation is mainly reflected in the relative abundance of metabolic pathways. These findings indicate that ultraviolet radiation in Plateau environment as an important influencing factor has an impact on microbial structure and metabolic pathways. This research provides an important theoretical basis for further understanding of water treatment ecosystem in Plateau environment, and also provides a new perspective for the development of water treatment ecosystem.

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