scholarly journals Skin bacterial communities of neotropical treefrogs vary with local environmental conditions at the time of sampling

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7044 ◽  
Author(s):  
Angie Estrada ◽  
Myra C. Hughey ◽  
Daniel Medina ◽  
Eria A. Rebollar ◽  
Jenifer B. Walke ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Temporal Variation ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Community Diversity ◽  
Amphibian Conservation ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Amphibian Skin

The amphibian skin microbiome has been the focus of recent studies aiming to better understand the role of these microbial symbionts in host defense against disease. However, host-associated microbial communities are complex and dynamic, and changes in their composition and structure can influence their function. Understanding temporal variation of bacterial communities on amphibian skin is critical for establishing baselines from which to improve the development of mitigation techniques based on probiotic therapy and provides long-term host protection in a changing environment. Here, we investigated whether microbial communities on amphibian skin change over time at a single site. To examine this, we collected skin swabs from two pond-breeding species of treefrogs, Agalychnis callidryas and Dendropsophus ebraccatus, over 4 years at a single lowland tropical pond in Panamá. Relative abundance of operational taxonomic units (OTUs) based on 16S rRNA gene amplicon sequencing was used to determine bacterial community diversity on the skin of both treefrog species. We found significant variation in bacterial community structure across long and short-term time scales. Skin bacterial communities differed across years on both species and between seasons and sampling days only in D. ebraccatus. Importantly, bacterial community structures across days were as variable as year level comparisons. The differences in bacterial community were driven primarily by differences in relative abundance of key OTUs and explained by rainfall at the time of sampling. These findings suggest that skin-associated microbiomes are highly variable across time, and that for tropical lowland sites, rainfall is a good predictor of variability. However, more research is necessary to elucidate the significance of temporal variation in bacterial skin communities and their maintenance for amphibian conservation efforts.

scholarly journals The leaf bacterial microbiota of female and male kiwifruit plants in distinct seasons: assessing the impact of Pseudomonas syringae pv. actinidiae

2021 ◽  
Author(s):  
Aitana Ares ◽  
Joana Pereira ◽  
Eva Garcia ◽  
Joana Costa ◽  
Igor Tiago
Keyword(s):  
Bacterial Community ◽  
Pseudomonas Syringae ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Defense Mechanisms ◽  
Abiotic Factors ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Sequencing Platform ◽  
The Impact

The pandemic Pseudomonas syringae pv. actinidiae (Psa) has been compromising the production of the kiwifruit industry in major producing countries. Abiotic factors and plant gender are known to influence the disease outcome. To better understand their impact, we have determined the diversity of the leafs bacterial communities using the V5-V6 region of the 16S rRNA gene amplicon on the Illumina MiSeq sequencing platform. Healthy and diseased female and male kiwifruit plants were analyzed in two consecutive seasons: spring and autumn. This work describes whether the season, plant gender and the presence of Psa can affect the leaves bacterial community. Fifty bacterial operational taxonomic units (OTUs) were identified and assigned to five phyla distributed by 14 different families and 23 genera. The leaves of healthy female and male kiwi plants share most of the identified bacterial populations, that undergoes major seasonal changes. In both cases a substantial increase of the relative abundance of genus Methylobacterium is observed in autumn. The presence of Psa induced profound changes on leaves bacterial communities structure translated into a reduction in the relative abundance of previously dominant genera that had been found in healthy plants, namely Hymenobacter, Sphingomonas and Massilia. The impact of Psa was less pronounced in the bacterial community structure of male plants in both seasons. Some of the naturally occurring genera have the potential to act as an antagonist or as enhancers of the defense mechanisms paving the way for environmentally friendly and sustainable disease control.

scholarly journals Uterine and vaginal bacterial community diversity prior to artificial insemination between pregnant and nonpregnant postpartum cows1

2019 ◽  
Vol 97 (10) ◽  
pp. 4298-4304 ◽  
Author(s):  
Taylor B Ault ◽  
Brooke A Clemmons ◽  
Sydney T Reese ◽  
Felipe G Dantas ◽  
Gessica A Franco ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Artificial Insemination ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Beef Cows ◽  
Community Diversity ◽  
Rrna Gene ◽  
Bacterial Community Diversity ◽  
Hypervariable Regions ◽  
Time Of Breeding

Abstract The present study evaluated the bovine vaginal and uterine bacterial community diversity and its relationship to fertility. Postpartum beef cows (n = 68) were synchronized beginning on day −21 and ending with timed artificial insemination (TAI) on day 0. Pregnancy was diagnosed 30 d after TAI. Uterine and vaginal flushes were collected on day −21, −9, and −2 for bacterial DNA extraction to sequence the V1 to V3 hypervariable regions of the 16S rRNA gene. Results indicated a decrease in the number of bacterial species over time in the uterus of resulting pregnant and nonpregnant beef cows (P < 0.0001). Principal coordinate analyses (PCoA) depicted clustering of samples, indicating closely related bacterial communities, by day in the uterus and vagina (P < 0.0001). At day −2, uterine samples from nonpregnant and pregnant animals clustered separately (P < 0.0001), with nonpregnant animal samples clustering tightly together. Overall, the current study suggests the shift in the reproductive bacterial communities’ diversity and phylogenetic relationship leading up to the time of breeding may contribute to successful pregnancy establishment.

scholarly journals Bacterial Communities in the Rhizosphere and Phyllosphere of Halophytes and Drought-Tolerant Plants in Mediterranean Ecosystems

2020 ◽  
Vol 8 (11) ◽  
pp. 1708
Author(s):  
Savvas Genitsaris ◽  
Natassa Stefanidou ◽  
Kleopatra Leontidou ◽  
Theodora Matsi ◽  
Katerina Karamanoli ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Properties ◽  
Bacterial Communities ◽  
Mediterranean Ecosystems ◽  
Community Diversity ◽  
Sampling Location ◽  
Rrna Gene ◽  
Sodic Soils ◽  
Drought Tolerant ◽  
Tolerant Plants

The aim of the study was to investigate the bacterial community diversity and structure by means of 16S rRNA gene high-throughput amplicon sequencing, in the rhizosphere and phyllosphere of halophytes and drought-tolerant plants in Mediterranean ecosystems with different soil properties. The locations of the sampled plants included alkaline, saline-sodic soils, acidic soils, and the volcanic soils of Santorini Island, differing in soil fertility. Our results showed high bacterial richness overall with Proteobacteria and Actinobacteria dominating in terms of OTUs number and indicated that variable bacterial communities differed depending on the plant’s compartment (rhizosphere and phyllosphere), the soil properties and location of sampling. Furthermore, a shared pool of generalist bacterial taxa was detected independently of sampling location, plant species, or plant compartment. We conclude that the rhizosphere and phyllosphere of native plants in stressed Mediterranean ecosystems consist of common bacterial assemblages contributing to the survival of the plant, while at the same time the discrete soil properties and environmental pressures of each habitat drive the development of a complementary bacterial community with a distinct structure for each plant and location. We suggest that this trade-off between generalist and specialist bacterial community is tailored to benefit the symbiosis with the plant.

scholarly journals Bacterial community structure upstream and downstream of cascade dams along the Lancang River in southwestern China

2020 ◽  
Vol 27 (34) ◽  
pp. 42933-42947
Author(s):  
Xia Luo ◽  
Xinyi Xiang ◽  
Guoyi Huang ◽  
Xiaorui Song ◽  
Peijia Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Community Diversity ◽  
Spatial Distance ◽  
Rrna Gene ◽  
Lancang River ◽  
Hydroelectric Dam ◽  
Cascade Dams

Abstract Extensive construction of dams by humans has caused alterations in flow regimes and concomitant alterations in river ecosystems. Even so, bacterioplankton diversity in large rivers influenced by cascade dams has been largely ignored. In this study, bacterial community diversity and profiles of seven cascade dams along the720 km of the Lancang River were studied using Illumina sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Spatiotemporal variations of bacterial communities in sediment and water of the Gongguoqiao hydroelectric dam and factors affecting these variations were also examined. Microbial diversity and richness in surface water increased slightly from upstream toward downstream along the river. A significant positive correlation between spatial distance and dissimilarities in bacterial community structure was confirmed (Mantel test, r = 0.4826, p = 0.001). At the Gongguoqiao hydroelectric dam, temporal differences in water overwhelmed spatial variability in bacterial communities. Temperature, precipitation, and nutrient levels were major drivers of seasonal microbial changes. Most functional groups associated with carbon cycling in sediment samples decreased from winter to summer. Our findings improve our understanding of associations, compositions, and predicted functional profiles of microbial communities in a large riverine ecosystem influenced by multiple cascade dams.

scholarly journals Variation in Sodic Soil Bacterial Communities Associated with Different Alkali Vegetation Types

2021 ◽  
Vol 9 (8) ◽  
pp. 1673
Author(s):  
Andrea K. Borsodi ◽  
Márton Mucsi ◽  
Gergely Krett ◽  
Attila Szabó ◽  
Tamás Felföldi ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Vegetation Types ◽  
Metabolic Potential ◽  
Sodic Soils ◽  
Sodic Soil ◽  
Strain Collection

In this study, we examined the effect of salinity and alkalinity on the metabolic potential and taxonomic composition of microbiota inhabiting the sodic soils in different plant communities. The soil samples were collected in the Pannonian steppe (Hungary, Central Europe) under extreme dry and wet weather conditions. The metabolic profiles of microorganisms were analyzed using the MicroResp method, the bacterial diversity was assessed by cultivation and next-generation amplicon sequencing based on the 16S rRNA gene. Catabolic profiles of microbial communities varied primarily according to the alkali vegetation types. Most members of the strain collection were identified as plant associated and halophilic/alkaliphilic species of Micrococcus, Nesterenkonia, Nocardiopsis, Streptomyces (Actinobacteria) and Bacillus, Paenibacillus (Firmicutes) genera. Based on the pyrosequencing data, the relative abundance of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes and Bacteroidetes also changed mainly with the sample types, indicating distinctions within the compositions of bacterial communities according to the sodic soil alkalinity-salinity gradient. The effect of weather extremes was the most pronounced in the relative abundance of the phyla Actinobacteria and Acidobacteria. The type of alkali vegetation caused greater shifts in both the diversity and activity of sodic soil microbial communities than the extreme aridity and moisture.

scholarly journals Early life skin microbial trajectory as a function of vertical and environmental transmission in Bornean foam-nesting frogs

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Sarah McGrath-Blaser ◽  
Morgan Steffen ◽  
T. Ulmar Grafe ◽  
María Torres-Sánchez ◽  
David S. McLeod ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Pond Water ◽  
Breeding Strategy ◽  
Skin Microbiome ◽  
Amphibian Skin ◽  
Environmental Interaction ◽  
Tadpole Skin ◽  
Foam Nest

Abstract Background The amphibian skin microbiome is an important mediator of host health and serves as a potential source of undiscovered scientifically significant compounds. However, the underlying modalities of how amphibian hosts obtain their initial skin-associated microbiome remains unclear. Here, we explore microbial transmission patterns in foam-nest breeding tree frogs from Southeast Asia (Genus: Polypedates) whose specialized breeding strategy allows for better delineation between vertically and environmentally derived microbes. To facilitate this, we analyzed samples associated with adult frog pairs taken after mating—including adults of each sex, their foam nests, environments, and tadpoles before and after environmental interaction—for the bacterial communities using DNA metabarcoding data (16S rRNA). Samples were collected from frogs in-situ in Brunei, Borneo, a previously unsampled region for amphibian-related microbial diversity. Results Adult frogs differed in skin bacterial communities among species, but tadpoles did not differ among species. Foam nests had varying bacterial community composition, most notably in the nests’ moist interior. Nest interior bacterial communities were discrete for each nest and overall displayed a narrower diversity compared to the nest exteriors. Tadpoles sampled directly from the foam nest displayed a bacterial composition less like the nest interior and more similar to that of the adults and nest exterior. After one week of pond water interaction the tadpole skin microbiome shifted towards the tadpole skin and pond water microbial communities being more tightly coupled than between tadpoles and the internal nest environment, but not to the extent that the skin microbiome mirrored the pond bacterial community. Conclusions Both vertical influence and environmental interaction play a role in shaping the tadpole cutaneous microbiome. Interestingly, the interior of the foam nest had a distinct bacterial community from the tadpoles suggesting a limited environmental effect on tadpole cutaneous bacterial selection at initial stages of life. The shift in the tadpole microbiome after environmental interaction indicates an interplay between underlying host and ecological mechanisms that drive community formation. This survey serves as a baseline for further research into the ecology of microbial transmission in aquatic animals.

scholarly journals Rhizosphere bacteria community and functions under typical natural halophyte communities in North China salinized areas

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259515
Author(s):  
Fating Yin ◽  
Fenghua Zhang ◽  
Haoran Wang
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Acid Metabolism ◽  
Rhizosphere Soil ◽  
Soil Bacterial Community ◽  
Rhizosphere Bacteria ◽  
Community Diversity ◽  
Rrna Gene ◽  
Soil Bacterial ◽  
Suaeda Glauca

Soil salinity is a serious environmental issue in arid China. Halophytes show extreme salt tolerance and are grow in saline-alkaline environments. There rhizosphere have complex bacterial communities, which mediate a variety of interactions between plants and soil. High-throughput sequencing was used to investigated rhizosphere bacterial community changes under the typical halophyte species in arid China. Three typical halophytes were Leymus chinensis (LC), Puccinellia tenuiflora (PT), Suaeda glauca (SG). The dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Acidobacteria and Bacteroidetes, Suaeda glauca rhizosphere has stronger enrichment of Nitrospirae and Cyanobacteria. The Ace, Chao and Shannon indices were significantly higher in soils under LC and SG (P<0.05). Functional predictions, based on 16S rRNA gene by PICRUSt, indicated that Energy metabolism, Amino acid metabolism, Carbohydrate metabolism and Fatty acid metabolism are dominant bacterial functions in three halophytes rhizosphere soil. Carbon metabolism, Oxidative phosphorylation, Methane metabolism, Sulfur metabolism and Nitrogen metabolism in SG were significantly higher than that in LC and PT. Regression analysis revealed that rhizosphere soil bacterial community structure is influenced by soil organic matter (SOM) and soil water content (SWC), while soil bacterial community diversity is affected by soil pH. This study contributes to our understanding of the distribution characteristics and metabolic functions under different halophyte rhizosphere bacterial communities, and will provide references for the use of rhizosphere bacteria to regulate the growth of halophytes and ecological restoration of saline soil.

Seasonal effects of river flow on microbial community coalescence and diversity in a riverine network

2020 ◽  
Vol 96 (8) ◽  
Author(s):  
Xia Luo ◽  
Xinyi Xiang ◽  
Yuanhao Yang ◽  
Guoyi Huang ◽  
Kaidao Fu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Flow Rate ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Rrna Gene ◽  
Strong Impact ◽  
Running Waters

ABSTRACT Terrestrial microbial communities may take advantage of running waters and runoff to enter rivers and mix with aquatic microorganisms. However, the environmental factors governing the interchange of the microbial community within a watercourse and its surrounding environment and the composition of the resulting community are often underestimated. The present study investigated the effect of flow rate on the mixing of water, soil, sediment and biofilm at four sites along the Lancang River and one branch of the river in winter and summer and, in turn, the resultant changes in the microbial community within each habitat. 16S rRNA gene-based Illumina high-throughput sequencing illustrated that bacterial communities were apparently distinct among biofilm, water, soil and sediment. Biofilms had the lowest richness, Shannon diversity and evenness indices compared with other habitats, and those three indices in all habitats increased significantly from winter to summer. SourceTracker analysis showed a significant coalescence between the bacterial communities of sediment, water and biofilm samples at lower flow rates. Additionally, the proportion of Betaproteobacteria in sediment and biofilms increased with a decrease in flow rate, suggesting the flow rate had a strong impact on microbial community composition and exchange among aquatic habitats. These results were further confirmed by a Mantel test and linear regression analysis. Microbial communities in all samples exhibited a significant but very weak distance–decay relationship (r = 0.093, P = 0.024). Turbidity played a much more important role on water bacterial community structure in summer (i.e. rainy season) (BIOENV, r = 0.92). Together, these results suggest that dispersal is an important factor affecting bacterial community structure in this system.

scholarly journals   Long-term agrichemical use leads to alterations in bacterial community diversity

2012 ◽  
Vol 58 (No. 10) ◽  
pp. 452-458 ◽  
Author(s):  
H. Tan ◽  
M. Barret ◽  
O. Rice ◽  
D.N. Dowling ◽  
J. Burke ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Spring Barley ◽  
Community Diversity ◽  
Rrna Gene ◽  
Soil Bacterial Communities ◽  
Culture Independent ◽  
Concomitant Reduction ◽  
Soil Bacterial

&nbsp; Bacterial communities are key drivers of soil fertility and agriculture productivity. Understanding how soil bacterial communities change in response to different conditions is an important aspect in the development of sustainable agriculture. There is a desire to reduce the current reliance on high inputs of chemicals and fertilisers in agriculture, but limited data are available on how this might impact soil bacterial communities. This study investigated the bacterial communities in a spring barley monoculture site subjected to two different input regimes for over 12 years: a conventional chemical/fertiliser regime, and a reduced input regime. A culture independent approach was performed to compare the bacterial communities through 16S rRNA gene PCR-DGGE. PCO analysis revealed that the rhizosphere has a strong structuring effect on the bacterial community. Moreover, high inputs of agrichemicals lead to an increase of phosphorus level in the soil and a concomitant reduction of the bacterial diversity. These results may help to evaluate the environmental risks associated with agrichemical usage. &nbsp;

scholarly journals Time after Time: Temporal Variation in the Effects of Grass and Forb Species on Soil Bacterial and Fungal Communities

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
S. Emilia Hannula ◽  
Anna M. Kielak ◽  
Katja Steinauer ◽  
Martine Huberty ◽  
Renske Jongen ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Temporal Variation ◽  
Microbial Communities ◽  
Plant Species ◽  
Bacterial Communities ◽  
Temporal Dynamics ◽  
Fungal Communities ◽  
Plant Soil ◽  
Soil Bacterial ◽  
Over Time

ABSTRACT Microorganisms are found everywhere and have critical roles in most ecosystems, but compared to plants and animals, little is known about their temporal dynamics. Here, we investigated the temporal stability of bacterial and fungal communities in the soil and how their temporal variation varies between grasses and forb species. We established 30 outdoor mesocosms consisting of six plant monocultures and followed microbial communities for an entire year in these soils. We demonstrate that bacterial communities vary greatly over time and that turnover plays an important role in shaping microbial communities. We further show that bacterial communities rapidly shift from one state to another and that this is related to changes in the relative contribution of certain taxa rather than to extinction. Fungal soil communities are more stable over time, and a large part of the variation can be explained by plant species and by whether they are grasses or forbs. Our findings show that the soil bacterial community is shaped by time, while plant group and plant species-specific effects drive soil fungal communities. This has important implications for plant-soil research and highlights that temporal dynamics of soil communities cannot be ignored in studies on plant-soil feedback and microbial community composition and function. IMPORTANCE Our findings highlight how soil fungal and bacterial communities respond to time, season, and plant species identity. We found that succession shapes the soil bacterial community, while plant species and the type of plant species that grows in the soil drive the assembly of soil fungal communities. Future research on the effects of plants on soil microbes should take into consideration the relative roles of both time and plant growth on creating soil legacies that impact future plants growing in the soil. Understanding the temporal (in)stability of microbial communities in soils will be crucial for predicting soil microbial composition and functioning, especially as plant species compositions will shift with global climatic changes and land-use alterations. As fungal and bacterial communities respond to different environmental cues, our study also highlights that the selection of study organisms to answer specific ecological questions is not trivial and that the timing of sampling can greatly affect the conclusions made from these studies.

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