scholarly journals Copper affects composition and functions of microbial communities in marine biofilms at environmentally relevant concentrations

2018 ◽  
Author(s):  
Natàlia Corcoll ◽  
Jianghua Yang ◽  
Thomas Backhaus ◽  
Xiaowei Zhang ◽  
Martin Karl Eriksson ◽  
...  
Keyword(s):  
Community Structure ◽  
Primary Production ◽  
Microbial Communities ◽  
Algal Biomass ◽  
Amplicon Sequencing ◽  
Quality Standard ◽  
Aquatic Communities ◽  
Static Test ◽  
Community Function ◽  
Eukaryotic Organisms

Cu pollution in coastal areas is a worldwide threat for aquatic communities. This study assesses the effects of Cu exposure on microbial diversity, community structure and functions of microbial communities in marine periphyton biofilms at environmental relevant concentrations. Periphyton was exposed for 18 days to five Cu concentrations, between 0.01 and 10 μM, in a semi-static test. Diversity and community structure of prokaryotic and eukaryotic organisms were assessed by 16S and 18S amplicon sequencing, respectively. Community function was studied as impacts on algal biomass and primary production. Additionally, we studied Pollution-Induced Community Tolerance (PICT) using photosynthesis as the endpoint. Sequencing results detected an average of 9504 and 1242 OTUs for 16S and 18S, respectively, reflecting the huge biodiversity of marine periphytic biofilms. Eukaryotes represent the most Cu-sensitive kingdom, where effects were seen already at concentrations as low as 10 nM. The structure of the prokaryotic part of the community was impacted at slightly higher concentrations (60 nM), which is still in the range of the Cu concentrations observed in the area (80 nM).The current environmental quality standard for Cu of 70 nM therefore does not seem to be sufficiently protective for periphyton. Cu exposure resulted in a more Cu-tolerant community, which was accompanied by a reduced total algal biomass, increased relative abundance of diatoms and a reduction of primary production. Cu exposure changed the network of associations between taxa in the communities. A total of 23 taxa, including species within Proteobacteria, Bacteroidetes, Stramenopiles and Hacrobia, were identified as being particularly sensitive to Cu. DNA metabarcoding is presented as a sensitive tool for community-level ecotoxicological studies that allows to observe impacts simultaneously on a multitude of pro- and eukaryotic species, and therefore to identify particularly sensitive, non-cultivable species and taxa.

scholarly journals Copper affects composition and functions of microbial communities in marine biofilms at environmentally relevant concentrations

2018 ◽  
Author(s):  
Natàlia Corcoll ◽  
Jianghua Yang ◽  
Thomas Backhaus ◽  
Xiaowei Zhang ◽  
Martin Karl Eriksson ◽  
...  
Keyword(s):  
Community Structure ◽  
Primary Production ◽  
Microbial Communities ◽  
Algal Biomass ◽  
Amplicon Sequencing ◽  
Quality Standard ◽  
Aquatic Communities ◽  
Static Test ◽  
Community Function ◽  
Eukaryotic Organisms

Cu pollution in coastal areas is a worldwide threat for aquatic communities. This study assesses the effects of Cu exposure on microbial diversity, community structure and functions of microbial communities in marine periphyton biofilms at environmental relevant concentrations. Periphyton was exposed for 18 days to five Cu concentrations, between 0.01 and 10 μM, in a semi-static test. Diversity and community structure of prokaryotic and eukaryotic organisms were assessed by 16S and 18S amplicon sequencing, respectively. Community function was studied as impacts on algal biomass and primary production. Additionally, we studied Pollution-Induced Community Tolerance (PICT) using photosynthesis as the endpoint. Sequencing results detected an average of 9504 and 1242 OTUs for 16S and 18S, respectively, reflecting the huge biodiversity of marine periphytic biofilms. Eukaryotes represent the most Cu-sensitive kingdom, where effects were seen already at concentrations as low as 10 nM. The structure of the prokaryotic part of the community was impacted at slightly higher concentrations (60 nM), which is still in the range of the Cu concentrations observed in the area (80 nM).The current environmental quality standard for Cu of 70 nM therefore does not seem to be sufficiently protective for periphyton. Cu exposure resulted in a more Cu-tolerant community, which was accompanied by a reduced total algal biomass, increased relative abundance of diatoms and a reduction of primary production. Cu exposure changed the network of associations between taxa in the communities. A total of 23 taxa, including species within Proteobacteria, Bacteroidetes, Stramenopiles and Hacrobia, were identified as being particularly sensitive to Cu. DNA metabarcoding is presented as a sensitive tool for community-level ecotoxicological studies that allows to observe impacts simultaneously on a multitude of pro- and eukaryotic species, and therefore to identify particularly sensitive, non-cultivable species and taxa.

scholarly journals High-throughput amplicon sequencing reveals the spatiotemporal effects, abiotic and biotic shaping factors for the microbial communities in tropical mangrove sediments in Sanya, China

2020 ◽  
Author(s):  
Wu Qu ◽  
Boliang Gao ◽  
Jie Wu ◽  
Min Jin ◽  
Jianxin Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Fungal Community ◽  
Amplicon Sequencing ◽  
Biotic Factors ◽  
Community Structures ◽  
Mangrove Sediments ◽  
Element Cycling ◽  
Microbial Community Structures

Abstract Background Microbial roles in element cycling and nutrient providing are crucial for mangrove ecosystems and serve as important regulators for climate change in Earth ecosystem. However, some key information about the spatiotemporal influences and abiotic and biotic shaping factors for the microbial communities in mangrove sediments remains lacking. Methods In this work, 22 sediment samples were collected from multiple spatiotemporal dimensions, including three locations, two depths, and four seasons, and the bacterial, archaeal, and fungal community structures in these samples were studied using amplicon sequencing. Results The microbial community structures were varied in the samples from different depths and locations based on the results of LDA effect size analysis, principal coordinate analysis, the analysis of similarities, and permutational multivariate ANOVA. However, these microbial community structures were stable among the seasonal samples. Linear fitting models and Mantel test showed that among the 13 environmental factors measured in this study, the sediment particle size (PS) was the key abiotic shaping factor for the bacterial, archaeal, or fungal community structure. Besides PS, salinity and humidity were also significant impact factors according to the canonical correlation analysis (p ≤ 0.05). Co-occurrence networks demonstrated that the bacteria assigned into phyla Ignavibacteriae, Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria were the key biotic factors for shaping the bacterial community in mangrove sediments. Conclusions This work showed the variability on spatial dimensions and the stability on temporal dimension for the bacterial, archaeal, or fungal microbial community structure, indicating that the tropical mangrove sediments are versatile but stable environments. PS served as the key abiotic factor could indirectly participate in material circulation in mangroves by influencing microbial community structures, along with salinity and humidity. The bacteria as key biotic factors were found with the abilities of photosynthesis, polysaccharide degradation, or nitrogen fixation, which were potential indicators for monitoring mangrove health, as well as crucial participants in the storage of mangrove blue carbons and mitigation of climate warming. This study expanded the knowledge of mangroves for the spatiotemporal variation, distribution, and regulation of the microbial community structures, thus further elucidating the microbial roles in mangrove management and climate regulation.

scholarly journals Press xenobiotic disturbance favors deterministic assembly with a shift in function and structure of bacterial communities in sludge bioreactors

2020 ◽  
Author(s):  
Ezequiel Santillan ◽  
Hari Seshan ◽  
Stefan Wuertz
Keyword(s):  
Community Structure ◽  
Bacterial Communities ◽  
Temporal Dynamics ◽  
Treatment Plant ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Batch Reactors ◽  
Function Structure ◽  
Community Function ◽  
And Function

AbstractDisturbance is thought to affect community assembly mechanisms, which in turn shape community structure and the overall function of the ecosystem. Here, we tested the effect of a continuous (press) xenobiotic disturbance on the function, structure, and assembly of bacterial communities within a wastewater treatment system. Two sets of four-liter sequencing batch reactors were operated in triplicate with and without the addition of 3-chloroaniline for a period of 132 days, following 58 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of bacterial community structure were derived from 16S rRNA gene amplicon sequencing. Community function, structure and assembly differed between press disturbed and undisturbed reactors. Temporal partitioning of assembly mechanisms via phylogenetic and non-phylogenetic null modelling analysis revealed that deterministic assembly prevailed for disturbed bioreactors, while the role of stochastic assembly was stronger for undisturbed reactors. Our findings are relevant because research spanning various disturbance types, environments and spatiotemporal scales is needed for a comprehensive understanding of the effects of press disturbances on assembly mechanisms, structure, and function of microbial communities.Graphical abstract

scholarly journals Depth and location influence prokaryotic and eukaryotic microbial community structure in New Zealand fjords

2019 ◽  
Author(s):  
Sven P. Tobias-Hünefeldt ◽  
Stephen R. Wing ◽  
Nadjejda Espinel-Velasco ◽  
Federico Baltar ◽  
Sergio E. Morales
Keyword(s):  
Community Structure ◽  
New Zealand ◽  
Microbial Communities ◽  
National Park ◽  
Amplicon Sequencing ◽  
Forested Catchments ◽  
Environmental Forcing ◽  
Low Salinity ◽  
The Impact ◽  
Depth View

SummarySystems with strong horizontal and vertical gradients, such as fjords, are useful models for studying environmental forcing. Here we examine microbial (prokaryotic and eukaryotic) community changes associated with the surface low salinity layer (LSL) and underlying seawater in multiple fjords in Fiordland National Park (New Zealand). High rainfall (1200-8000 mm annually) and linked runoff from native forested catchments results in surface LSLs with high tannin concentrations within each fjord. These gradients are expected to drive changes in microbial communities. We used amplicon sequencing (16S and 18S) to assess the impact of these gradients on microbial communities and identified depth linked changes in diversity and community structure. With increasing depth we observed significant increases in Proteobacteria (15%) and SAR (37%), decreases in Opisthokonta (35%), and transiently increased Bacteroidetes (3% increase from 0 to 40 m, decreasing by 8% at 200 m). Community structure differences were observed along a transect from inner to outer regions, specifically 25% mean relative abundance decreases in Opisthokonta and Bacteroidetes, and increases in SAR (25%) and Proteobacteria (>5%) at the surface, indicating changes based on distance from the ocean. This provides the first in-depth view into the ecological drivers of microbial communities within New Zealand fjords.

scholarly journals Living Lithic and Sublithic Bacterial Communities in Namibian Drylands

2021 ◽  
Vol 9 (2) ◽  
pp. 235
Author(s):  
Steffi Genderjahn ◽  
Simon Lewin ◽  
Fabian Horn ◽  
Anja M. Schleicher ◽  
Kai Mangelsdorf ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Soil Formation ◽  
Amplicon Sequencing ◽  
Mineral Weathering ◽  
Rrna Gene ◽  
Rock Weathering ◽  
Weathering Processes ◽  
Rock Types ◽  
Culture Independent

Dryland xeric conditions exert a deterministic effect on microbial communities, forcing life into refuge niches. Deposited rocks can form a lithic niche for microorganisms in desert regions. Mineral weathering is a key process in soil formation and the importance of microbial-driven mineral weathering for nutrient extraction is increasingly accepted. Advances in geobiology provide insight into the interactions between microorganisms and minerals that play an important role in weathering processes. In this study, we present the examination of the microbial diversity in dryland rocks from the Tsauchab River banks in Namibia. We paired culture-independent 16S rRNA gene amplicon sequencing with culture-dependent (isolation of bacteria) techniques to assess the community structure and diversity patterns. Bacteria isolated from dryland rocks are typical of xeric environments and are described as being involved in rock weathering processes. For the first time, we extracted extra- and intracellular DNA from rocks to enhance our understanding of potentially rock-weathering microorganisms. We compared the microbial community structure in different rock types (limestone, quartz-rich sandstone and quartz-rich shale) with adjacent soils below the rocks. Our results indicate differences in the living lithic and sublithic microbial communities.

scholarly journals Microbial stowaways – waterbirds as dispersal vectors of aquatic pro- and microeukaryotic communities

2021 ◽  
Author(s):  
Beáta Szabó ◽  
Attila Szabó ◽  
Csaba F Vad ◽  
Emil Boros ◽  
Dunja Lukić ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Compositional Variation ◽  
Rrna Gene ◽  
Aquatic Habitats ◽  
Aquatic Communities ◽  
Anser Anser ◽  
Filter Feeder ◽  
Waterbird Species ◽  
Dispersal Vectors

Aim: Waterbirds are important dispersal vectors of multicellular organisms such as macrophytes, aquatic macroinvertebrates, and zooplankton. However, no study to date has focused on their potential role in dispersing aquatic microbial communities. Here, we carried out the first explicit study on passive transport (endozoochory) of prokaryotes and unicellular microeukaryotes by waterbirds based on a metagenomic approach. By directly comparing the dispersed set of organisms to the source pool of a natural metacommunity, we aimed for a realistic estimate of the overall importance of waterbird zoochory for natural microbial communities. Location: Seewinkel region of Austria and Hungary. Taxon: Prokaryotes and unicellular microeukaryotes. Methods: In 2017 and 2018, water samples from natural aquatic habitats along with fresh droppings of the dominant greylag goose (Anser anser) and four other waterbird species were collected in a well-delineated habitat network of temporary saline ponds (soda pans). Their prokaryotic and microeukaryotic communities were identified via 16S and 18S rRNA gene amplicon sequencing and compared across years and waterbird species. Results: We found that up to 40% of the dominant aquatic microbial OTUs were transported by A. anser. OTU richness in A. anser droppings was lower, but compositional variation was higher compared to the aquatic communities, probably resulting from stochastic pick-up of microbes from multiple aquatic habitats. We furthermore found that prokaryote species composition of bird droppings followed the interannual turnover in the aquatic communities. Finally, we found species-specific differences among different waterbird species. Among them, the planktivore filter-feeder northern shovelers (Anas clypeata) collected and dispersed a more species-rich subset of microeukaryotes than shorebirds or geese. Main conclusions: Overall, our study provides the first quantitative empirical evidence of endozoochory in natural microorganism communities. These results imply that waterbirds may be crucial in maintaining ecological connectivity between discrete aquatic habitats at the level of microbial communities. Keywords: aquatic microorganisms, bacteria, connectivity, dispersal, endozoochory, phytoplankton, protists, waterbirds

scholarly journals Predicting the structure and function of coalesced microbial communities

2017 ◽  
Author(s):  
Pawel Sierocinski ◽  
Kim Milferstedt ◽  
Florian Bayer ◽  
Tobias Großkopf ◽  
Mark Alston ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Methane Production ◽  
Structure And Function ◽  
Recent Theory ◽  
Simple Method ◽  
Average Performance ◽  
Community Function ◽  
And Function

ABSTRACTMicrobial communities commonly coalesce in nature, but the consequences for resultant community structure and function is unclear. Consistent with recent theory, we demonstrate using methanogenic communities that the most productive communities in isolation dominated when communities were mixed. As a corollary of this dynamic, total methane production increased with the number of inoculated communities. The cohesion and dominance of single communities was explained by more “niche-packed” communities being both more efficient at exploiting resources and resistant to invasion, rather than a function of the average performance of component species. These results are likely to be relevant to the ecological dynamics of natural microbial communities, as well as demonstrating a simple method to predictably enhance microbial community function in biotechnology, health and agriculture.

Comparative fungal community analyses using metatranscriptomics and ITS-amplicon sequencing from Norway spruce

2021 ◽  
Author(s):  
Andreas Schneider ◽  
John Sundh ◽  
Görel Sundström ◽  
Kerstin Richau ◽  
Nicolas Delhomme ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Norway Spruce ◽  
Environmental Samples ◽  
Marker Gene ◽  
Amplicon Sequencing ◽  
Fungal Communities ◽  
Individual Species ◽  
Rna Seq ◽  
Sequencing Data

<p>Microbial communities are major players in carbon and nitrogen cycling globally and are of particular importance for plant communities in the nutrient poor soils of boreal forests. Especially relevant are the fungal communities in the soil that interact with the plants in multiple ways, indirectly through their pivotal role in the breakdown of organic matter and, more directly, through mycorrhizal symbiosis with plant roots. Large-scale disturbances of these complex microbial communities can lead to shifts in soil carbon storage with unknown and global-scale long-term consequences. To understand the dynamics of these communities and their relationship to associated plants in response to climate change and anthropogenic influence, we need a better understanding of how modern “omics” methods can help us to understand compositional and functional shifts of these microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from environmental samples. In contrast, currently phylogenetic marker gene amplicon sequencing data is generally used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in RNA-Seq transcriptomic data from matched samples. Here we describe fungal communities using both RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from mature stands of the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient deficient) and nutrient enriched plots at the Flakaliden forest research site in boreal northern Sweden. We created an assembly-based, reproducible and hardware agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data.<strong> </strong>We show that the community structure indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying limitations imposed by current database coverage. Furthermore, we show examples to demonstrate how metatranscriptomics data additionally provides biologically informative functional insight at the community and individual species level. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response and effect both between host plants and their associated microbial communities, and among the members of microbial communities in environmental samples in general.</p>

scholarly journals Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kazutoshi Yoshitake ◽  
Gaku Kimura ◽  
Tomoko Sakami ◽  
Tsuyoshi Watanabe ◽  
Yukiko Taniuchi ◽  
...  
Keyword(s):  
Time Series ◽  
Microbial Communities ◽  
Pacific Coast ◽  
Three Dimensional ◽  
Amplicon Sequencing ◽  
Metagenomic Data ◽  
Shotgun Metagenomics ◽  
Functional Features ◽  
Pacific Coast Of Japan ◽  
Marine Microbial Communities

AbstractAlthough numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird’s-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.

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