scholarly journals Reef location has a greater impact than coral bleaching severity on the microbiome of Pocillopora acuta

Coral Reefs ◽  
2021 ◽  
Author(s):  
Emmanuelle S. Botté ◽  
Neal E. Cantin ◽  
Véronique J. L. Mocellin ◽  
Paul A. O’Brien ◽  
Melissa M. Rocker ◽  
...  
Keyword(s):  
Heat Stress ◽  
Microbial Communities ◽  
Coral Bleaching ◽  
Health Indicators ◽  
Amplicon Sequencing ◽  
Coral Community ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bleaching Event ◽  
The Impact

AbstractCoral reefs are increasingly threatened by heat stress events leading to coral bleaching. In 2016, a mass bleaching event affected large parts of the Great Barrier Reef (GBR). Whilst bleaching severity and coral mortality are usually monitored throughout major bleaching events, other health indicators, such as changes in microbial partners, are rarely assessed. We examined the impact of the 2016 bleaching event on the composition of the microbial communities in the coral Pocillopora acuta at Havannah Island Pandora reef, separated by 12 km on the inshore central GBR. Corals experienced moderate heat stress (3.6 and 5.3 degree heating weeks), inducing major bleaching (30–60%) at the coral community level. Samples were partitioned according to Symbiodiniaceae densities into three bleaching severity categories (mild, moderate, and severe). Whilst Symbiodiniaceae densities were similar at both reef locations, sequencing of the Symbiodiniaceae ITS2 and prokaryotic 16S rRNA genes revealed that microbial communities were significantly different between reefs, but not according to bleaching severity. Symbiodiniaceae composition was dominated by the genus Cladocopium with low abundances of Durusdinium detected in moderately and severely bleached colonies at both sites, despite site-specific ITS2 profiles. Bacterial communities were dominated by Proteobacteria and were almost entirely lacking the common Pocilloporid associate Endozoicomonas regardless of bleaching severity. Strikingly, only 11.2% of the bacterial Amplicon Sequencing Variants (ASVs) were shared between sites. This reef specificity was driven by 165 ASVs, mainly from the family Rhodobacteraceae. Comparison with previous studies suggests that the moderate heat stress experienced on the central GBR in 2016 caused the near-complete absence of Endozoicomonas. Symbiodiniaceae and bacteria (particularly Rhodobacteraceae) can be vertically transmitted in P. acuta, and larval propagation can be spatially restricted for this brooding species. Our results demonstrate that, unlike bleaching severity, location-specific factors and species-specific life history traits might have been paramount in shaping the P. acuta microbiome.

scholarly journals Impact of Soil Drying-Rewetting Stress on Microbial Communities and Activities and on Degradation of Two Crop Protection Products

2004 ◽  
Vol 70 (5) ◽  
pp. 2577-2587 ◽  
Author(s):  
Manuel Pesaro ◽  
Gilles Nicollier ◽  
Josef Zeyer ◽  
Franco Widmer
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Stress Responses ◽  
Crop Protection ◽  
16S Rrna Genes ◽  
Cell Counting ◽  
Rrna Genes ◽  
Soil Dna ◽  
Degradation Rates ◽  
The Impact

ABSTRACT Prior to registration of crop protection products (CPPs) their persistence in soil has to be determined under defined conditions. For this purpose, soils are collected in the field and stored for up to 3 months prior to the tests. During storage, stresses like drying may induce changes in microbiological soil characteristics (MSCs) and thus may influence CPP degradation rates. We investigated the influence of soil storage-related stress on the resistance and resilience of different MSCs by assessing the impact of a single severe drying-rewetting cycle and by monitoring recovery from this event for 34 days. The degradation and mineralization of the fungicide metalaxyl-M and the insecticide lufenuron were delayed by factors of 1.5 to 5.4 in the dried and rewetted soil compared to the degradation and mineralization in an undisturbed reference. The microbial biomass, as estimated by direct cell counting and from the soil DNA content, decreased on average by 51 and 24%, respectively. The bulk microbial activities, as determined by measuring substrate-induced respiration and fluorescein diacetate hydrolysis, increased after rewetting and recovered completely within 6 days after reequilibration. The effects on Bacteria, Archaea, and Pseudomonas were investigated by performing PCR amplification of 16S rRNA genes and reverse-transcribed 16S rRNA, followed by restriction fragment length polymorphism (RFLP) and terminal RFLP (T-RFLP) fingerprinting. Statistical analyses of RFLP and T-RFLP profiles indicated that specific groups in the microbial community were sensitive to the stress. In addition, evaluation of rRNA genes and rRNA as markers for monitoring the stress responses of microbial communities revealed overall similar sensitivities. We concluded that various structural and functional MSCs were not resistant to drying-rewetting stress and that resilience depended strongly on the parameter investigated.

scholarly journals Impact of Helicobacter Pylori Infection on Duodenal Microbial Community Structure and Microbial Metabolic Pathways

2021 ◽  
Author(s):  
Tadashi Maeda ◽  
Hiroaki Zai ◽  
Yuto Fukui ◽  
Yoshifumi Kato ◽  
Eri Kumade ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
16S Rrna ◽  
Metabolic Pathways ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
H Pylori ◽  
The Impact

Abstract Background The bioactivities of commensal duodenal microbiota greatly influence the biofunction of hosts. We investigated the role of Helicobacter pylori infection in extra-gastroduodenal diseases by determining the impact of H. pylori infection on the duodenal microbiota. We sequenced 16S rRNA genes in samples aspirated from the descending duodenum of 47 (male, 20; female, 27) individuals who were screened for gastric cancer. Samples were analysed using 16S rRNA gene amplicon sequencing, and the LEFSe and Kyoto Encyclopaedia of Genes and Genomes methods were used to determine whether the duodenal microflora and microbial biofunctions were affected using H. pylori infection. Results Thirteen and 34 participants tested positive and negative for H. pylori, respectively. We identified 1,404 bacterial operational taxonomic units from 23 phyla and 253 genera. H. pylori infection increased the relative mean abundance of Proteobacteria and Neisseria and decreased the abundance of the two other phyla (Actinobacteria and TM7) and nine genera (Rothia, TM7-3, Leptotrichia, Lachnospiraceae, Megasphaera, F16, Moryella, Filifactor, and Paludibacter). Microbiota features were significantly influenced in H. pylori-positive participants by 12 taxa mostly classified as Gammaproteobacteria. Microbial functional annotation revealed that H. pylori significantly affected 12 microbial metabolic pathways. Conclusions H. pylori disrupted normal bacterial communities in the duodenum and changed the biofunctions of commensal microbiota primarily by upregulating specific metabolic pathways. Such upregulation may be involved in the onset of diseases associated with H. pylori infection.

scholarly journals Arable agriculture changes soil microbial communities in the South African Grassland Biome

2018 ◽  
Vol 114 (5/6) ◽  
Author(s):  
Gilbert Kamgan Nkuekam ◽  
Don A. Cowan ◽  
Angel Valverde
Keyword(s):  
Microbial Communities ◽  
Agricultural Soils ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
The Impact ◽  
Natural Grassland

Many studies, mostly in temperate regions of the northern hemisphere, have demonstrated that agricultural practices affect the composition and diversity of soil microbial communities. However, very little is known about the impact of agriculture on the microbial communities in other regions of the world, most particularly on the African continent. In this study, we used MiSeq amplicon sequencing of bacterial 16S rRNA genes and fungal ITS regions to characterise microbial communities in agricultural and natural grassland soils located in the Mpumalanga Province of South Africa. Nine soil chemical parameters were also measured to evaluate the effects of edaphic factors on microbial community diversity. Bacterial and fungal communities were significantly richer and more diverse in natural grassland than in agricultural soils. Microbial taxonomic composition was also significantly different between the two habitat types. The phylum Acidobacteria was significantly more abundant in natural grassland than in agricultural soils, while Actinobacteria and the family Nectriaceae showed the opposite pattern. Soil pH and phosphorus significantly influenced bacterial communities, whereas phosphorus and calcium influenced fungal communities. These findings may be interpreted as a negative impact of land-use change on soil microbial diversity and composition.

scholarly journals Iron and sulfate reduction structure microbial communities in (sub-)Antarctic sediments

2021 ◽  
Author(s):  
Lea C. Wunder ◽  
David A. Aromokeye ◽  
Xiuran Yin ◽  
Tim Richter-Heitmann ◽  
Graciana Willis-Poratti ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Sulfate Reduction ◽  
Marine Sediments ◽  
Iron Reduction ◽  
Environmental Changes ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Geochemical Parameters ◽  
Dissimilatory Iron Reduction ◽  
The Impact

AbstractPermanently cold marine sediments are heavily influenced by increased input of iron as a result of accelerated glacial melt, weathering, and erosion. The impact of such environmental changes on microbial communities in coastal sediments is poorly understood. We investigated geochemical parameters that shape microbial community compositions in anoxic surface sediments of four geochemically differing sites (Annenkov Trough, Church Trough, Cumberland Bay, Drygalski Trough) around South Georgia, Southern Ocean. Sulfate reduction prevails in Church Trough and iron reduction at the other sites, correlating with differing local microbial communities. Within the order Desulfuromonadales, the family Sva1033, not previously recognized for being capable of dissimilatory iron reduction, was detected at rather high relative abundances (up to 5%) while other members of Desulfuromonadales were less abundant (<0.6%). We propose that Sva1033 is capable of performing dissimilatory iron reduction in sediment incubations based on RNA stable isotope probing. Sulfate reducers, who maintain a high relative abundance of up to 30% of bacterial 16S rRNA genes at the iron reduction sites, were also active during iron reduction in the incubations. Thus, concurrent sulfate reduction is possibly masked by cryptic sulfur cycling, i.e., reoxidation or precipitation of produced sulfide at a small or undetectable pool size. Our results show the importance of iron and sulfate reduction, indicated by ferrous iron and sulfide, as processes that shape microbial communities and provide evidence for one of Sva1033’s metabolic capabilities in permanently cold marine sediments.

Bioinformatics Analysis of The Rhizosphere Microbiota of Dangshan Su Pear in Different Soil Types

2020 ◽  
Vol 15 (5) ◽  
pp. 503-514
Author(s):  
Xiaojing Ma ◽  
Sambhaji Balaso Thakar ◽  
Huimin Zhang ◽  
Zequan Yu ◽  
Li Meng ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Terrestrial Ecosystems ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Types ◽  
Plant Materials ◽  
Microbial Structures

Background: The rhizosphere microbiota are of vital importance for plant growth and health in terrestrial ecosystems. There have been extensive studies aiming to identify the microbial communities as well as their relationship with host plants in different soil types. Objective: In the present study, we have employed the high-throughput sequencing technology to investigate the composition and structure of rhizosphere microbiota prosperous at the root of Dangshan Su pear growing in sandy soil and clay soil. Methods: A high-throughput amplicon sequencing survey of the bacterial 16S rRNA genes and fungal ITS regions from rhizosphere microbiota was firstly performed. Subsequently, several common bacterial and fungal communities were found to be essential to Dangshan Su pear by using a series of bioinformatics and statistics tools. Finally, the soil-preferred microbiota were identified through variance analysis and further characterized in the genus level. Result: Dangshan Su pears host rich and diverse microbial communities in thin layer of soil adhering to their roots. The composition of dominant microbial phyla is similar across different soil types, but the quantity of each microbial community varies significantly. Specially, the relative abundance of Firmicutes increases from 9.69% to 61.66% as the soil ecosystem changes from clay to sandy, which can be not only conducive to the degradation of complex plant materials, but also responsible for the disinfestation of pathogens. Conclusion: Our results have a symbolic significance for the potential efforts of rhizosphere microbiota on the soil bioavailability and plant health. Through selecting soil types and altering microbial structures, the improvement of fruit quality of Dangshan Su pear is expected to be achieved.

scholarly journals Coupling Root Diameter With Rooting Depth to Reveal the Heterogeneous Assembly of Root-Associated Bacterial Communities in Soybean

2021 ◽  
Vol 12 ◽  
Author(s):  
Wen Luo ◽  
Xiaoyu Zai ◽  
Jieyu Sun ◽  
Da Li ◽  
Yuanli Li ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Plant Root ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Root Diameter ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rooting Depth

Root diameter and rooting depth lead to morphological and architectural heterogeneity of plant roots; however, little is known about their effects on root-associated microbial communities. Bacterial community assembly was explored across 156 samples from three rhizocompartments (the rhizosphere, rhizoplane, and endosphere) for different diameters (0.0–0.5 mm, 0.5–1.0 mm, 1.0–2.0 mm, and&gt;2.0 mm) and depths (0–5 cm, 5–10 cm, 10–15 cm, and 15–20 cm) of soybean [Glycine max (L.) Merrill] root systems. The microbial communities of all samples were analyzed using amplicon sequencing of bacterial 16S rRNA genes. The results showed that root diameter significantly affected the rhizosphere and endosphere bacterial communities, while rooting depth significantly influenced the rhizosphere and rhizoplane bacterial communities. The bacterial alpha diversity decreased with increasing root diameter in all three rhizocompartments, and the diversity increased with increasing rooting depth only in the rhizoplane. Clearly, the hierarchical enrichment process of the bacterial community showed a change from the rhizosphere to the rhizoplane to the endosphere, and the bacterial enrichment was higher in thinner or deeper roots (except for the roots at a depth of 15–20 cm). Network analysis indicated that thinner or deeper roots led to higher bacterial network complexity. The core and keystone taxa associated with the specific root diameter class and rooting depth class harbored specific adaptation or selection strategies. Root diameter and rooting depth together affected the root-associated bacterial assembly and network complexity in the root system. Linking root traits to microbiota may enhance our understanding of plant root-microbe interactions and their role in developing environmentally resilient root ecosystems.

scholarly journals An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Denise M. O’Sullivan ◽  
Ronan M. Doyle ◽  
Sasithon Temisak ◽  
Nicholas Redshaw ◽  
Alexandra S. Whale ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Relative Abundance ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Microbiome Analysis ◽  
The Impact

AbstractDespite the advent of whole genome metagenomics, targeted approaches (such as 16S rRNA gene amplicon sequencing) continue to be valuable for determining the microbial composition of samples. Amplicon microbiome sequencing can be performed on clinical samples from a normally sterile site to determine the aetiology of an infection (usually single pathogen identification) or samples from more complex niches such as human mucosa or environmental samples where multiple microorganisms need to be identified. The methodologies are frequently applied to determine both presence of micro-organisms and their quantity or relative abundance. There are a number of technical steps required to perform microbial community profiling, many of which may have appreciable precision and bias that impacts final results. In order for these methods to be applied with the greatest accuracy, comparative studies across different laboratories are warranted. In this study we explored the impact of the bioinformatic approaches taken in different laboratories on microbiome assessment using 16S rRNA gene amplicon sequencing results. Data were generated from two mock microbial community samples which were amplified using primer sets spanning five different variable regions of 16S rRNA genes. The PCR-sequencing analysis included three technical repeats of the process to determine the repeatability of their methods. Thirteen laboratories participated in the study, and each analysed the same FASTQ files using their choice of pipeline. This study captured the methods used and the resulting sequence annotation and relative abundance output from bioinformatic analyses. Results were compared to digital PCR assessment of the absolute abundance of each target representing each organism in the mock microbial community samples and also to analyses of shotgun metagenome sequence data. This ring trial demonstrates that the choice of bioinformatic analysis pipeline alone can result in different estimations of the composition of the microbiome when using 16S rRNA gene amplicon sequencing data. The study observed differences in terms of both presence and abundance of organisms and provides a resource for ensuring reproducible pipeline development and application. The observed differences were especially prevalent when using custom databases and applying high stringency operational taxonomic unit (OTU) cut-off limits. In order to apply sequencing approaches with greater accuracy, the impact of different analytical steps needs to be clearly delineated and solutions devised to harmonise microbiome analysis results.

scholarly journals Assessing population collapse of Drupella spp. (Mollusca: Gastropoda) 2 years after a coral bleaching event in the Republic of Maldives

Hydrobiologia ◽  
2021 ◽  
Author(s):  
L. Saponari ◽  
I. Dehnert ◽  
P. Galli ◽  
S. Montano
Keyword(s):  
Coral Bleaching ◽  
Prey Availability ◽  
Coral Cover ◽  
Environmental Data ◽  
High Plasticity ◽  
Bleaching Event ◽  
Coral Recovery ◽  
The Republic ◽  
The Impact ◽  
Line Intercept

AbstractCorallivory causes considerable damage to coral reefs and can exacerbate other disturbances. Among coral predators, Drupella spp. are considered as delayer of coral recovery in the Republic of Maldives, although little information is available on their ecology. Thus, we aimed to assess their population structure, feeding behaviour and spatial distribution around 2 years after a coral bleaching event in 2016. Biological and environmental data were collected using belt and line intercept transects in six shallow reefs in Maldives. The snails occurred in aggregations with a maximum of 62 individuals and exhibited a preference for branching corals. Yet, the gastropods showed a high plasticity in adapting feeding preferences to prey availability. Drupella spp. were homogenously distributed in the study area with an average of 9.04 ± 19.72 ind/200 m2. However, their occurrence was significantly different at the reef scale with the highest densities found in locations with higher coral cover. The impact of Drupella spp. appeared to be minimal with the population suffering from the loss of coral cover. We suggest that monitoring programs collect temporal- and spatial-scale data on non-outbreaking populations or non-aggregating populations to understand the dynamics of predation related to the co-occurrence of anthropogenic and natural impacts.

scholarly journals Coordination of microbe–host homeostasis by crosstalk with plant innate immunity

Nature Plants ◽  
2021 ◽  
Author(s):  
Ka-Wai Ma ◽  
Yulong Niu ◽  
Yong Jia ◽  
Jana Ordon ◽  
Charles Copeland ◽  
...  
Keyword(s):  
Growth Inhibition ◽  
Amplicon Sequencing ◽  
Host Susceptibility ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Root Growth Inhibition ◽  
Natural Soil ◽  
Molecular Pattern ◽  
Immune Related Genes ◽  
Molecular Patterns

AbstractPlants grown in natural soil are colonized by phylogenetically structured communities of microbes known as the microbiota. Individual microbes can activate microbe-associated molecular pattern (MAMP)-triggered immunity (MTI), which limits pathogen proliferation but curtails plant growth, a phenomenon known as the growth–defence trade-off. Here, we report that, in monoassociations, 41% (62 out of 151) of taxonomically diverse root bacterial commensals suppress Arabidopsis thaliana root growth inhibition (RGI) triggered by immune-stimulating MAMPs or damage-associated molecular patterns. Amplicon sequencing of bacterial 16S rRNA genes reveals that immune activation alters the profile of synthetic communities (SynComs) comprising RGI-non-suppressive strains, whereas the presence of RGI-suppressive strains attenuates this effect. Root colonization by SynComs with different complexities and RGI-suppressive activities alters the expression of 174 core host genes, with functions related to root development and nutrient transport. Furthermore, RGI-suppressive SynComs specifically downregulate a subset of immune-related genes. Precolonization of plants with RGI-suppressive SynComs, or mutation of one commensal-downregulated transcription factor, MYB15, renders the plants more susceptible to opportunistic Pseudomonas pathogens. Our results suggest that RGI-non-suppressive and RGI-suppressive root commensals modulate host susceptibility to pathogens by either eliciting or dampening MTI responses, respectively. This interplay buffers the plant immune system against pathogen perturbation and defence-associated growth inhibition, ultimately leading to commensal–host homeostasis.

scholarly journals Ultra-accurate microbial amplicon sequencing with synthetic long reads

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Benjamin J. Callahan ◽  
Dmitry Grinevich ◽  
Siddhartha Thakur ◽  
Michael A. Balamotis ◽  
Tuval Ben Yehezkel
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strain Identification ◽  
Long Reads ◽  
Long Read

Abstract Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. Methods Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. Results LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. Conclusions The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics.

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