scholarly journals Metagenomic Characterization Reveals Pronounced Seasonality in the Diversity and Structure of the Phyllosphere Bacterial Community in a Mediterranean Ecosystem

2019 ◽  
Vol 7 (11) ◽  
pp. 518 ◽  
Author(s):  
Despoina Vokou ◽  
Savvas Genitsaris ◽  
Katerina Karamanoli ◽  
Katerina Vareli ◽  
Marina Zachari ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput Sequencing ◽  
Bacterial Colonization ◽  
The Other ◽  
Mediterranean Ecosystem ◽  
Seasonal Differences ◽  
Operational Taxonomic Units ◽  
Seasonal Environment ◽  
Habitat Specialists ◽  
Taxonomic Groups

We explore how the phyllosphere microbial community responds to a very seasonal environment such as the Mediterranean. For this, we studied the epiphytic bacterial community of a Mediterranean ecosystem in summer and winter, expecting to detect seasonal differences at their maximum. With high-throughput sequencing (HTS), we detected the operational taxonomic units (OTUs) present in the phyllosphere and also in the surrounding air. The epiphytic community is approximately five orders of magnitude denser than the airborne one and is made almost exclusively by habitat specialists. The two communities differ considerably but Proteobacteria and Actinobacteria are dominant in both. Of the five most abundant phyllosphere OTUs, two were closely related to Sphingomonas strains, one to Methylobacterium and the other two to Rhizobiales and Burkholderiales. We found the epiphytic community to become much richer, more distinct, even and diverse, denser and more connected in summer. In contrast, there was no difference in the level of bacterial colonization of the phyllosphere between the two seasons, although there were seasonal differences for individual taxonomic groups: Firmicutes, Gemmatimonadetes and Chlroroflexi had a higher participation in summer, whereas the major Proteobacteria classes presented reverse patterns, with Betaproteobacteria increasing in summer at the expense of the prominent Alphaproteobacteria.

scholarly journals Endosymbiotic Rickettsiella causes cytoplasmic incompatibility in a spider host

2020 ◽  
Author(s):  
Laura C. Rosenwald ◽  
Michael I. Sitvarin ◽  
Jennifer A. White
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Bacterial Strain ◽  
High Throughput Sequencing ◽  
Cytoplasmic Incompatibility ◽  
The Other ◽  
Bacterial Endosymbionts ◽  
Different Strains

AbstractMany arthropod hosts are infected with bacterial endosymbionts that manipulate host reproduction, but few bacterial taxa have been shown to cause such manipulations. Here we show that a bacterial strain in the genus Rickettsiella causes cytoplasmic incompatibility (CI) between infected and uninfected hosts. We first surveyed the bacterial community of the agricultural spider Mermessus fradeorum (Linyphiidae) using high throughput sequencing and found that individual spiders can be infected with up to five different strains of maternally-inherited symbiont from the genera Wolbachia, Rickettsia, and Rickettsiella. The Rickettsiella strain was pervasive, found in all 23 tested spider matrilines. We used antibiotic curing to generate uninfected matrilines that we reciprocally crossed with individuals infected only with Rickettsiella. We found that only 13% of eggs hatched when uninfected females were mated with Rickettsiella-infected males; in contrast, at least 83% of eggs hatched in the other cross types. This is the first documentation of Rickettsiella, or any Gammaproteobacteria, causing CI. We speculate that induction of CI may be much more widespread among maternally-inherited bacteria than previously appreciated. Further, our results reinforce the importance of thoroughly characterizing and assessing the inherited microbiome before attributing observed host phenotypes to well-characterized symbionts such as Wolbachia.

scholarly journals Environmental characteristics and changes of bacterial communities in the meltwater runoff of glacier in Ny-Alesund, Arctic

2021 ◽  
Author(s):  
Lidong Lin ◽  
Nengfei Wang ◽  
Wenbing Han ◽  
Botao Zhang ◽  
Jiaye Zang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Operational Taxonomic Units ◽  
The Core ◽  
Meltwater Runoff ◽  
Glacial Runoff ◽  
Weighted Correlation

Abstract The present study assessed the diversity and composition of bacterial communities in glacial runoff and glacial soils in the Midre Lovénbreen glacier region of Svalbard. A total of 6,593 operational taxonomic units were identified by high-throughput sequencing. The results showed differences in bacterial community composition between the upper and lower reaches of glacial runoff. The abundance of Actinobacteria, Firmicutes, Betaproteobacteria and Gammaproteobacteria in the upper reaches of glacial runoff was higher than that in the lower reaches. In contrast, the the abundance of Cyanobacteria and Alphaproteobacteria in the downstream of glacial runoff was higher than that in the upstream. In addition, we compared bacterial diversity and composition between glacial runoff areas and soils. The chart analysis showed that bacterial diversity in glacial soil was higher than that in the glacial runoff. Some typical bacteria in the soil, such as Actinobacteria, entered glacial runoff through contact between them. The abundance of Acidobacteria, Sphingobacterium and Flavobacterium was higher in glacial soil. Weighted correlation network analysis showed that the core bacteria in glacial runoff and glacial soil were typical bacteria in different habitats. Distance-based redundancy analysis revealed that NO 2 - -N was the most significant factor affecting the distribution of soil bacterial community, while NO 3 - -N was the most significant factor affecting the distribution of glacial runoff bacterial community.

Role of Yeasts in the Cranberry Fruit Rot Disease Complex

Plant Disease ◽  
2020 ◽  
Author(s):  
Zachary David Zalewski ◽  
Rae Page ◽  
Richard Lankau ◽  
Patricia McManus
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
The Other ◽  
Fruit Rot ◽  
Internal Transcribed Spacer Region ◽  
Operational Taxonomic Units ◽  
Inhibition Of Growth ◽  
Hanseniaspora Uvarum ◽  
Rot Disease

Cranberry fruit rot (CFR) is an economically important disease caused by at least 10 species of filamentous fungi. Despite the application of fungicides, incidence of CFR is sometimes high, raising the possibility of a role for microbes other than fungi in the CFR complex. Isolation of microbes from rotten berries on media that favor either bacteria or yeasts resulted in mucoid colonies from fewer than 15% of dry-harvested rotten berries but up to 60% of wet-harvested berries. The mucoid colonies were identified as yeasts, primarily in the family Saccharomycetaceae. Inoculation of sound berries with three yeasts, Hanseniaspora uvarum, Pichia fermentans, and Pichia terricola, resulted in significantly higher incidence and severity of rot symptoms compared to mock-inoculated controls; these yeasts were recovered from inoculated berries, providing evidence of their pathogenicity. The minimum concentrations of azoxystrobin, chlorothalonil, and prothioconazole that resulted in 80% inhibition of growth compared to untreated controls (MIC80) were determined for a subset of yeasts. In general, MIC80s were higher for azoxystrobin and prothioconazole (usually >64 µg/ml) than for chlorothalonil (usually ≤1 µg/ml). To complement culture-dependent studies, DNA was isolated from wet- and dry-harvested rotten berries, and fungi were identified to the level of family by high-throughput sequencing of the fungal internal transcribed spacer region (ITS2). There were no fungal families consistently detected among samples by one method (culturing or high-throughput sequencing) and missed by the other that have not previously been reported in cranberry; however, some fungal families were found to be more abundant by one method versus the other. Harvest method (wet or dry) had a significant effect on the composition of fungal communities of rotten berries (P < 0.001), and operational taxonomic units representing the Saccharomycetaceae were more abundant in wet- than dry-harvested berries. Taken together, the results suggest that some yeasts are pathogenic to cranberry and may be especially relevant in wet-harvested berries.

scholarly journals The gut bacterial diversity of sheep associated with different breeds in Qinghai province

2020 ◽  
Author(s):  
Jianjun Chang ◽  
Xiaoting Yao ◽  
Chenxiang Zuo ◽  
Yuxu Qi ◽  
Dekun Chen ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput Sequencing ◽  
The Other ◽  
Principal Coordinates Analysis ◽  
Qinghai Province ◽  
Microbiome Composition ◽  
Sheep Breeds ◽  
Principal Coordinates ◽  
Tibetan Sheep ◽  
Nmds Analysis

Abstract Background: Gut microbiota play important roles in their co-evolution with mammals. However, little is understood about gut bacterial community of Tibetan sheep compared with other sheep breeds. In this study, we investigated the gut bacterial community in 4 different sheep breeds living in the Qinghai-Tibetan Plateau (QTP) of China using high-throughput sequencing (HTS) technique. Results: The results suggested that bacterial community abundance and breeds diversity of Tibetan sheep (TS) were significantly lower than that of the other three breeds of sheep [Dorset sheep (DrS), Dorper sheep (DrS) and Small Tail Han sheep (STHS)] (p < 0.05). Principal coordinates analysis (PCoA) and nonmetric multidimensional scaling (NMDS) analysis indicated that microbiome composition of TS was significantly different from that of other three sheep breeds (p < 0.01). Firmicutes was the most predominant microbial phylum in the gut, followed by Bacteroidetes. The gut bacterial community of TS showed higher proportions of phylum Spirochaetes, Proteobacteria and Verrucomicrobia, compared to the other three sheep breeds, but the Deferribacteres was absent in TS. At the genus level, Treponema, Succinivibrio, 5-7N15 and Prevotella showed significantly higher abundance in TS than in the other three sheep breeds (p < 0.05). Conclusions: In this study, we first employed HTS to understand the gut microbiomes among different sheep breeds in QTP of China.

scholarly journals Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape

2019 ◽  
Author(s):  
Bryan N. Nguyen ◽  
Elaine W. Shen ◽  
Janina Seemann ◽  
Adrienne M.S. Correa ◽  
James L. O’Donnell ◽  
...  
Keyword(s):  
Community Composition ◽  
Environmental Dna ◽  
Invertebrate Community ◽  
Ecological Processes ◽  
Operational Taxonomic Units ◽  
Invertebrate Diversity ◽  
Visual Survey ◽  
Habitat Specialists ◽  
Taxonomic Groups

AbstractAccurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Environmental DNA (eDNA) surveys show promise as a way to effectively characterize fine-scale patterns of community composition, but most studies to date have evaluated its effectiveness in single habitats and for conspicuous taxonomic groups in temperate ecosystems. We tested whether a single PCR survey of eDNA in seawater using a broad metazoan primer could identify differences in community composition between five adjacent habitats at 19 sites across a tropical Caribbean bay in Panama. We paired this effort with visual fish surveys to compare methods for a conspicuous taxonomic group. eDNA revealed a tremendous diversity of animals (8,586 operational taxonomic units), including many small taxa that would be undetected in traditional in situ surveys. Fish comprised only 0.07% of the taxa detected by a broad COI primer, yet included 43 species not observed in the visual survey. eDNA revealed significant differences in fish and invertebrate community composition across adjacent habitats and areas of the bay driven in part by taxa known to be habitat-specialists or tolerant to wave action. Our results demonstrate the ability of broad eDNA surveys to identify biodiversity patterns in the ocean.

scholarly journals Endosymbiotic Rickettsiella causes cytoplasmic incompatibility in a spider host

2020 ◽  
Vol 287 (1930) ◽  
pp. 20201107 ◽  
Author(s):  
Laura C. Rosenwald ◽  
Michael I. Sitvarin ◽  
Jennifer A. White
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Bacterial Strain ◽  
High Throughput Sequencing ◽  
Cytoplasmic Incompatibility ◽  
The Other ◽  
Bacterial Endosymbionts ◽  
Different Strains

Many arthropod hosts are infected with bacterial endosymbionts that manipulate host reproduction, but few bacterial taxa have been shown to cause such manipulations. Here, we show that a bacterial strain in the genus Rickettsiella causes cytoplasmic incompatibility (CI) between infected and uninfected hosts. We first surveyed the bacterial community of the agricultural spider Mermessus fradeorum (Linyphiidae) using high throughput sequencing and found that individual spiders can be infected with up to five different strains of maternally inherited symbiont from the genera Wolbachia , Rickettsia , and Rickettsiella . The Rickettsiella strain was pervasive, found in all 23 tested spider matrilines. We used antibiotic curing to generate uninfected matrilines that we reciprocally crossed with individuals infected only with Rickettsiella . We found that only 13% of eggs hatched when uninfected females were mated with Rickettsiella -infected males; in contrast, at least 83% of eggs hatched in the other cross types. This is the first documentation of Rickettsiella , or any Gammaproteobacteria, causing CI. We speculate that induction of CI may be much more widespread among maternally inherited bacteria than previously appreciated. Further, our results reinforce the importance of thoroughly characterizing and assessing the inherited microbiome before attributing observed host phenotypes to well-characterized symbionts such as Wolbachia .

scholarly journals The gut bacterial diversity of sheep associated with different breeds in Qinghai province

2020 ◽  
Author(s):  
Jianjun Chang ◽  
Xiaoting Yao ◽  
Chenxiang Zuo ◽  
Yuxu Qi ◽  
Dekun Chen ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput Sequencing ◽  
The Other ◽  
Principal Coordinates Analysis ◽  
Qinghai Province ◽  
Microbiome Composition ◽  
Sheep Breeds ◽  
Principal Coordinates ◽  
Tibetan Sheep ◽  
Nmds Analysis

Abstract Background: Gut microbiota play important roles in their co-evolution with mammals. However, little is understood about gut bacterial community of Tibetan sheep compared with other sheep breeds. In this study, we investigated the gut bacterial community in 4 different sheep breeds living in the Qinghai-Tibetan Plateau (QTP) of China using high-throughput sequencing (HTS) technique. Results: The results suggested that bacterial community abundance and breeds diversity of Tibetan sheep (TS) were significantly lower than that of the other three breeds of sheep [Dorset sheep (DrS), Dorper sheep (DrS) and Small Tail Han sheep (STHS)] (p < 0.05). Principal coordinates analysis (PCoA) and nonmetric multidimensional scaling (NMDS) analysis indicated that microbiome composition of TS was significantly different from that of other three sheep breeds (p < 0.01). Firmicutes was the most predominant microbial phylum in the gut, followed by Bacteroidetes. The gut bacterial community of TS showed higher proportions of phylum Spirochaetes, Proteobacteria and Verrucomicrobia, compared to the other three sheep breeds, but the Deferribacteres was lacked in TS. At the genus level, Treponema, Succinivibrio, 5-7N15 and Prevotella showed significantly higher abundance in TS than in the other three sheep breeds (p < 0.05). Conclusions: In this study, we first employed HTS to fully understand the gut microbiomes among different sheep breeds in QTP of China.

scholarly journals Metagenomic Characterization of Bacterial Communities on Ready-to-Eat Vegetables and Effects of Household Washing on their Diversity and Composition

Pathogens ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 37 ◽  
Author(s):  
Soultana Tatsika ◽  
Katerina Karamanoli ◽  
Hera Karayanni ◽  
Savvas Genitsaris
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Human Pathogens ◽  
Storage Duration ◽  
Point Of Sale ◽  
Operational Taxonomic Units ◽  
High Level

Ready-to-eat (RTE) leafy salad vegetables are considered foods that can be consumed immediately at the point of sale without further treatment. The aim of the study was to investigate the bacterial community composition of RTE salads at the point of consumption and the changes in bacterial diversity and composition associated with different household washing treatments. The bacterial microbiomes of rocket and spinach leaves were examined by means of 16S rRNA gene high-throughput sequencing. Overall, 886 Operational Taxonomic Units (OTUs) were detected in the salads’ leaves. Proteobacteria was the most diverse high-level taxonomic group followed by Bacteroidetes and Firmicutes. Although they were processed at the same production facilities, rocket showed different bacterial community composition than spinach salads, mainly attributed to the different contributions of Proteobacteria and Bacteroidetes to the total OTU number. The tested household decontamination treatments proved inefficient in changing the bacterial community composition in both RTE salads. Furthermore, storage duration of the salads at refrigeration temperatures affected the microbiome, by decreasing the bacterial richness and promoting the dominance of psychrotropic bacteria. Finally, both salads were found to be a reservoir of opportunistic human pathogens, while washing methods usually applied at home proved to be inefficient in their removal.

scholarly journals Community Structure and Function of Epiphytic Bacteria Associated With Myriophyllum spicatum in Baiyangdian Lake, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Lei Sun ◽  
Jiashuo Wang ◽  
Yangyang Wu ◽  
Tianyu Gao ◽  
Cunqi Liu
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Myriophyllum Spicatum ◽  
Epiphytic Bacteria ◽  
Baiyangdian Lake ◽  
Operational Taxonomic Units ◽  
The Common ◽  
And Function

Epiphytic bacteria on the surfaces of submerged macrophytes play important roles in the growth of the host plant, nutrient cycling, and the conversion of pollutants in aquatic systems. A knowledge of the epiphytic bacterial community structure could help us to understand these roles. In this study, the abundance, diversity, and functions of the epiphytic bacterial community of Myriophyllum spicatum collected from Baiyangdian Lake in June, August, and October 2019 were studied using quantitative PCR (qPCR), high-throughput sequencing, and the prediction of functions. An analysis using qPCR showed that the epiphytic bacteria were the most abundant in October and the least abundant in August. High-throughput sequencing revealed that Proteobacteria, Gammaproteobacteria, and Aeromonas were the dominant phylum, class, and genus in all the samples. The common analyses of operational taxonomic units (OTUs), NMDS, and LDA showed that the epiphytic bacterial communities were clustered together based on the seasons. The results of a canonical correlation analysis (CCA) showed that the key water quality index that affected the changes of epiphytic bacterial community of M. spicatum was the total phosphorus (TP). The changes in abundance of Gammaproteobacteria negatively correlated with the TP. Predictive results from FAPROTAX showed that the predominant biogeochemical cycle functions of the epiphytic bacterial community were chemoheterotrophy, nitrate reduction, and fermentation. These results suggest that the epiphytic bacterial community of M. spicatum from Baiyangdian Lake varies substantially with the seasons and environmental conditions.

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